We just released a new version of qBase with new features and bug
fixes, and an updated manual.
We recommend to install the new version by going to the qBase download
page, and typing your email adress and qBase download password that
you previously obtained.
http://medgen.ugent.be/qbase/download.php

The zip-file containing all the files to be updated (including the
manual) should be extracted to the folder in which qBase was
installed, thereby overwriting the older files. After installation and
start-up, the qBase start screen should show version 1.1.0.

Changes in version 1.1.0:
    - geNorm input file generation (for determination of stably
expressed reference genes using the geNorm software)
    - Normalization factor (NF) histogram
    - Reference gene quality evaluation
    - Manual updated and accessible from within qBase
    - Horizontal scroll bars in the Analyzer module to scroll through
large graphs
    - Long run names trimming to fit within the cells
    - Simultaneous use of NTCs and NACs no longer results in an 'NTC
problem' alert
    - Occasional problems related to removing experiments/projects
solved
    - More informative error messages during run import
    - Data import possibility using universal qBase format
    - Importer is compatible with Opticon Monitor files from version 1
to 3.1

Enjoy qBase!

Jan Hellemans
Jo Vandesompele

Some users experience severe problems with qBase, and are not even
able to analyze the VHL experiment example.  This is a known bug of
qBase which occurs only on a small number of PC's (4/350 users have
reported this problem).  We do not encounter this problem on our PC's
which makes it a hard bug to solve.  Therefore, for the moment we can
only suggest to try qBase on another PC if you still want to use it.

If you encounter this problem, please notify us at qbase@...,
especially if you have some VBA skills which could help solve the
problem.  After all qBase is still an open source project for which we
hope to receive help and comments from the community.

Jan

Hello,
I use a MyIQ software and I try to use qBase but with no success.

The VHL example doesn't work:
I can't analyse the VHL example. When I try to do it, Excel stops
working and stays on the workflow.

I'm not able to import data:
When I try to import my results, I can read this message: "An error
occured while attempting to reorder data".
I tried to modify my data (excel files) in many many (many...) ways but
it still doesn't work.

I hope somebody might help me to solve these problems. Maybe it's about
excel or windows...(I'm working with  "windows 2000 pro" and "office
2000")

Thank you for your help

Dear Dr. A. Schiel
The manual/previously-messege-replies states that the import file
should look EXACTLY like it does in the manual.. I've discovered
that the export(copy-paste) files from the quantification tab in the
MyIQ software doesnt set the header "Identifier" adjusted to the left
(Aligned to the left) of the cell, as shown in the manual. I got the
exaclty same error as you, Dr. A. Schiel, but after adjusted
the "Identifier" header to the left, qBase works perfectly. Compare
the exampel file(VHL1) with your own. Hope this helped.



//Andreas






--- In qBase@yahoogroups.com, "kolipidos" <SchielAnjaE@n...> wrote:
> Dear,
> after reading the posted messages I could recreate all of the
> problems posted with importing data.
>
> I use a MyIQ-BioRad machine and my output files look exactly as
they
> should according to the manual.
> When I try to import them I get the well known "An error occured
> while attempting to reorder data".
> When I try to import the VHL-example file I get the "Run-time
> error '1004'".
> When I try to analyze the existing VHL.xls in the browser the
> computer hangs up.
>
> I seriuosly doubt that these problems have anything to do with the
> PCR software but if necessary I could provide the MyIQ-software
> (works stand alone).
>
> Since I am not the only one with the problem that already the
first
> step of importing data is not working it seems to me that maybe
> Excel is the problem and additional information on how Excel has
to
> be set up might help.
>
> And by any chance might ther be a Linux compatible version of
qBase?
>
> Sincerely,
> Dr. A. Schiel,
> LUMC
> Leiden
> The Netherlands

Dear,
after reading the posted messages I could recreate all of the
problems posted with importing data.

I use a MyIQ-BioRad machine and my output files look exactly as they
should according to the manual.
When I try to import them I get the well known "An error occured
while attempting to reorder data".
When I try to import the VHL-example file I get the "Run-time
error '1004'".
When I try to analyze the existing VHL.xls in the browser the
computer hangs up.

I seriuosly doubt that these problems have anything to do with the
PCR software but if necessary I could provide the MyIQ-software
(works stand alone).

Since I am not the only one with the problem that already the first
step of importing data is not working it seems to me that maybe
Excel is the problem and additional information on how Excel has to
be set up might help.

And by any chance might ther be a Linux compatible version of qBase?

Sincerely,
Dr. A. Schiel,
LUMC
Leiden
The Netherlands

You could use the non-parametric equivalent of the t-test, e.g. the
Mann-Whitney U, or a randomization test.

Jo

privsky wrote:

> Okey, i am confused about this matter.
>
>
> I have two different samples. One is 5 untreated/control samples (same
> kind) and the other is a 50 treated samples (same kind). I wonder what
> kind of statistic methods i can use to compare the results between
> them? I don't think that i can use ANOVA, since they need at least 3
> different samples.
>
>
> Besides i can not use T-test or Z-test either, since the former needs
> both samples to be at a small number n<30, while the latter needs both
> samples to be large n>30. My samples is n=5 (controll samples) and
> n=50 (treated samples).
>
>
>
> Thank you!

hello,
I just download the qBase software but unfortunately I do not
understand well the operation of the software... is there French among
the members of this group which could help me by telephone?
thank you so much

Okey, i am confused about this matter.


I have two different samples. One is 5 untreated/control samples (same
kind) and the other is a 50 treated samples (same kind). I wonder what
kind of statistic methods i can use to compare the results between
them? I don't think that i can use ANOVA, since they need at least 3
different samples.


Besides i can not use T-test or Z-test either, since the former needs
both samples to be at a small number n<30, while the latter needs both
samples to be large n>30. My samples is n=5 (controll samples) and
n=50 (treated samples).



Thank you!

Dear,

We are aware of the fact that importing data is sometimes troublesome.  This is
mainly because we did not have the software from every manufacturer (working on)
and often had to base our import code on a single file we received form
colleagues.  Therefore, whenever encountering problems during import send us a
copy of the file you are trying to import and specify the equipment and software
used to generate the file.  This will allow us to correct errors and improve the
  import procedures.

It is hard to help you out with the second problem since we have not seen it
here before.  Does any error message pop up?  Perhaps the spinning cursor
indicates an endless loop.  To check this: press Ctrl+Break, this will stop the
code and prompt you with the question what to do, select the button which will
direct you to the VBA code.  If you copy and send us the code around your
cursor, we might be able to track and solve the problem.

Best regards,
Jan

Quoting e_cattell <e_cattell@...>:

> qBase sounds like a fabulous way to manage real time data but I simply cant
> get it to
> work.  Firstly when I import my data from a Rotergene 3000 data file I get
> the message run
> time error 1004 with the message 'application defined or object defined
> error'.   I have
> read through the other messages on this site and checked the column headings
> as
> advised, but they were fine.  I also find that if I hit analyse even for the
> sample VHL data,
> the flow chart appears, but I am left with a spinning cursor that eventually
> crashes the
> computer.  Am I doing anything really obvious wrong?
>
>
>
>
>
> Yahoo! Groups Links
>
>
>
>
>
>
>


--

qBase sounds like a fabulous way to manage real time data but I simply cant get
it to
work.  Firstly when I import my data from a Rotergene 3000 data file I get the
message run
time error 1004 with the message 'application defined or object defined error'.
I have
read through the other messages on this site and checked the column headings as
advised, but they were fine.  I also find that if I hit analyse even for the
sample VHL data,
the flow chart appears, but I am left with a spinning cursor that eventually
crashes the
computer.  Am I doing anything really obvious wrong?

Whenever errors occur during import take a careful look at the
requirements for the input files in the manual.  The column headers
have to be exactly as stated in the manual, additional columns are
ignored.

In your case the column header Ct should probably be renamed to
"Threshold Cycle       Ct".

Good luck,
Jan

--- In qBase@yahoogroups.com, "damienpalomo" <damienpalomo@y...> wrote:
> hello,
> when I want to import my exel folder I met an error 1004...and it says
> me that an error occur during the columns rearengement...
> I work with the IQ Icycler
> My fold contains 4 columns : well, Ct, set point and identifier...
> I also try to put in the exel folder others columns but I've always the
> same problem!!
>
> I've you got an idea to resolve this error?...
>
> thank you for help me
> Damien

hello,
when I want to import my exel folder I met an error 1004...and it says
me that an error occur during the columns rearengement...
I work with the IQ Icycler
My fold contains 4 columns : well, Ct, set point and identifier...
I also try to put in the exel folder others columns but I've always the
same problem!!

I've you got an idea to resolve this error?...

thank you for help me
Damien

Hello everybody
When I try to import a csv result run, I have a message 'error 1004'.
I use an ABI Prism 7000.
Otherwise, my export table contain 'Standard deviation' on the 6th
column, 'Quantity' being on the 7th one (no values in this column).
I've deleted the 'Standard deviation' column to have 'Quantity' on
column 6, but it doesn't change anything.
Any idea?
Many thanks in advance.
Denis

Hi Jan,

Thanks for your reply. After trying different things I was finally able to
successfully import
the VHL file under the Icycler option in the import window. However I still
cannot make ABI
7500 file work, it must be something to do with the ABI 7500 file. I will send
the excel file
to you. Anyway this is exactly what I am doing.

Double click on the qbase file. Enable macros when asked. qBase browser window
then
opens. Start a new project by clicking on the Project + icon. Start a new
experiment by
clicking on the Experiment + icon. Click on the Run + icon. The run window pops
up. Click
on the import run data button. In the import screen, with my file I have tried
all the listed
ABI options plus the other options as well. However as I explained yesterday I
get the error
message saying "Could not order data". Today after I was able to successfully
load the VHL
file, I looked at that file and manually tried to configure my data to look like
that but still
could not get it to import under any option regardless whether it was in the
Excel format
or the CVS format.

Thanks for your help.

Best Regards,

Rizwan

I cannot import run data. Error message says "Error occured while attempting to
re order
data". Interestingly I have tried to import the sample VHL file and get the same
message. I
am using ABI 7500 and the CVS file generated by the machine contains all the
listed
headings (in addition to several other ) in a header column. I have also created
an excel
file with just the WELL, SAMPLE, DETECTOR, TASK AND Ct headings but still no
luck.
Ofcourse since I can't load the sample file the problems probably is not the
header. Any
suggestions will be appreciated.

Regards,

Rizwan Hamid

Hello! I am a MJ real-time PCR user.
The analysis software is upgraded to 3.1, recently.
So I can not easy to import the data to qbase!
Could you help me to modifiy the data import format?
I already upload the new format on the Files!
Thank you for your help!
This software is great!

Jan,

Thank you for your answer.

I sent you an original file using the SDS2.1 software from Applied
Biosystems. Every run exported has this file format . I didn't modify any
row or colomns.
I can send you some other exported files with more datas to help you.
By waiting, I'm going to correct my original files according to your
advise to continue my analyses.

Have a good day
Best regards,

Manu

--- In qBase@yahoogroups.com, Jan Hellemans <jan.hellemans@g...> wrote:
> Dear Manu,
>
> We looked at your file and it doesn't quite look like the one we used
> for creating the import module.  The file we had contained some
> information lines, the column headers, the data block and again some
> information lines.  Your file contains several data blocks with
> headers and closing info lines.  qBase only imports the first data
> block and this causes your problems.  Could you tell us whether this
> is an original export file, or one you constructed yourself by
> combining several data files?  If this is a true export then we need
> to adjust our import module for the ABI7900.  In the mean while these
> kinds of files can be imported, after having corrected them to contain
> only one data block.  This can be done by retaining only the header
> for the first data block and the closing lines from the last data
> block.  In between these only data (and no empty lines) should be
> present.
>
> Please report this kinds of errors to qbase@m... in the future.
>
> Best regards,
> Jan

Dear Manu,

We looked at your file and it doesn't quite look like the one we used
for creating the import module.  The file we had contained some
information lines, the column headers, the data block and again some
information lines.  Your file contains several data blocks with
headers and closing info lines.  qBase only imports the first data
block and this causes your problems.  Could you tell us whether this
is an original export file, or one you constructed yourself by
combining several data files?  If this is a true export then we need
to adjust our import module for the ABI7900.  In the mean while these
kinds of files can be imported, after having corrected them to contain
only one data block.  This can be done by retaining only the header
for the first data block and the closing lines from the last data
block.  In between these only data (and no empty lines) should be
present.

Please report this kinds of errors to qbase@... in the future.

Best regards,
Jan

Jan,
I selected this option to import plates.I tried with other 384 runs.
But in ExpMain sheet I don't have all my samples and my genes. and
when I'm going to the plate view, I see a plate in 96 format.
So I will send you my export run. (qPCR-ProjetVC- Manip n34 Aiolos
TaqMan -6t6g_130505.txt)
Best regards
Manu


--- In qBase@yahoogroups.com, Jan Hellemans <jan.hellemans@g...> wrote:
> Dear Manu,
>
> In order to use 384 ABI7900 plates in qBase, you have to select the
> 384 option while importing plates.  If you used this option but still
> have the problem, try selecting another plate within the same
> experiment.  If this does not help please export the project and send
> it over so we can use it for debugging qBase and gettting rid of these
> annoying problems.
>
> Best regards,
> Jan
>
> On 6/23/05, norby_manu <elouis@s...> wrote:
> >  Hi,
> >  I'm working on ABI 7900. And always in 384 well format.
> >  I imported experiments in qBase from 384 well runs. But in "Run
Editor
> >  view" I see a 96 plate format. So some samples and genes are
disappeared.
> >  I used 122 wells out of 384.
> >  Could you explain me how could I do to solve this problem ?
> >
> >  All the best.
> >  Manu
> >
> >
> >
> >
> >
> >  ________________________________
> >  Yahoo! Groups Links
> >
> >
> > To visit your group on the web, go to:
> > http://groups.yahoo.com/group/qBase/
> >
> > To unsubscribe from this group, send an email to:
> > qBase-unsubscribe@yahoogroups.com
> >
> > Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.

Dear Manu,

In order to use 384 ABI7900 plates in qBase, you have to select the
384 option while importing plates.  If you used this option but still
have the problem, try selecting another plate within the same
experiment.  If this does not help please export the project and send
it over so we can use it for debugging qBase and gettting rid of these
annoying problems.

Best regards,
Jan

On 6/23/05, norby_manu <elouis@...> wrote:
>  Hi,
>  I'm working on ABI 7900. And always in 384 well format.
>  I imported experiments in qBase from 384 well runs. But in "Run Editor
>  view" I see a 96 plate format. So some samples and genes are disappeared.
>  I used 122 wells out of 384.
>  Could you explain me how could I do to solve this problem ?
>
>  All the best.
>  Manu
>
>
>
>
>
>  ________________________________
>  Yahoo! Groups Links
>
>
> To visit your group on the web, go to:
> http://groups.yahoo.com/group/qBase/
>
> To unsubscribe from this group, send an email to:
> qBase-unsubscribe@yahoogroups.com
>
> Your use of Yahoo! Groups is subject to the Yahoo! Terms of Service.

Hi,
I'm working on ABI 7900. And always in 384 well format.
I imported experiments in qBase from 384 well runs. But in "Run Editor
view" I see a 96 plate format. So some samples and genes are disappeared.
I used 122 wells out of 384.
Could you explain me how could I do to solve this problem ?

All the best.
Manu

Hi Eric,

Detector would be the gene name, and Task the sample type (Unknown,
Standard, NTC).

Note:
- not UNKN but Unknown
- if no Ct value could be determined (threshold is not passed), the Ct
value is "Undetermined".

Jo


ericprina wrote:

> Hello,
> I'm working with a LightCycler (relative quantification).
> I would like to use the ABI7900 file format (384 wells) to import my data.
> The headers row described in qBase manual includes :Well / Sample /
> Detector (???) / Task (???) / Ct.
> Where should I include the type of sample (UNKN for all) and the name
> of the gene ???
> Thank you for your help.
> Eric

We just released a bug fix version (1.0.1) and updated the manual.
We recommend to install the new version by going to the qBase download
page, and typing your email adress and qBase download password that
you previously obtained.
http://medgen.ugent.be/qbase/download.php

The zip-file containing all the files to be updated (including the
manual) should be extracted to the folder in which qBase was
installed, thereby overwriting the older files. After installation and
start-up, the qBase start screen should show version 1.0.1.

Changes in version 1.0.1:
- Accelerated closing of the Browser module
- Modified start-up screen to include hyperlinks for the website /
discussion forum / e-mail
- License accessible from within the start and about screens
- About screen included in the Browser
- 'Delete' button disabled in the Browser to avoid problems/errors
- Worksheet browsing tabs removed in the Analyzer to avoid
problems/errors
- Import module for the MX3000 corrected
- Identifier field information extraction added for MX3000 and Opticon
Monitor files
- Trailing spaces in iCycler well identifiers automatically removed
- Rotorgene data import automatically converts well numbering into
plate (row-column) well names
- Table and graph can be printed on a single page
- Manual revision

Good luck!

Jan Hellemans
Jo Vandesompele

We are working on a solution for qBase to run on the Mac platform. No
guarantee that it will work, and no idea when it will be ready (at
least a few weeks).
Thank you for your patience.

Jo

--- In qBase@yahoogroups.com, "Steven Young MD, PhD"
<steve.young@m...> wrote:
> Same problem on my mac.
> -Steve
>
> --- In qBase@yahoogroups.com, "matt_nev" <matthew.neville@o...> wrote:
> > Just tried qbase with the macintosh Excel from the latest Office
2004 but got an
> Automation
> > problem error message.  Anyone else out there using a Mac and
having problems.
> >
> > Matt

Hello,
I'm working with a LightCycler (relative quantification).
I would like to use the ABI7900 file format (384 wells) to import my data.
The headers row described in qBase manual includes :Well / Sample /
Detector (???) / Task (???) / Ct.
Where should I include the type of sample (UNKN for all) and the name
of the gene ???
Thank you for your help.
Eric

Same problem on my mac.
-Steve

--- In qBase@yahoogroups.com, "matt_nev" <matthew.neville@o...> wrote:
> Just tried qbase with the macintosh Excel from the latest Office 2004 but got
an
Automation
> problem error message.  Anyone else out there using a Mac and having problems.
>
> Matt

--- In qBase@yahoogroups.com, "eliwanag2000" <eliwanag2000@y...> wrote:
> I am using lightcycler which is not included in your list of data
> transfer formats, can I still use qBase to analyze my data.  Is it
> possible to enter data manually.
>
> Thanks,
>
> eliwanag2000

Users with qPCR equipment not included in the list of supported
formats can still use qBase if they manually convert the input data
into any of the supported formats.  At the end of the manual a
description is given about the layout of all the supported formats.
It is recommended to contact qbase@... and to deliver us
with some of your input files.  These will allow us to write an
additional import procedure for the missing qPCR equipment.

Jan Hellemans

I am using lightcycler which is not included in your list of data
transfer formats, can I still use qBase to analyze my data.  Is it
possible to enter data manually.

Thanks,

eliwanag2000

Just tried qbase with the macintosh Excel from the latest Office 2004 but got an
Automation
problem error message.  Anyone else out there using a Mac and having problems.

Matt