Dear all, We now have a new dChip user group at here: http://groups.google.com/group/dchip-software <http://groups.google.com/group/dchip-software> Also,...
2747
Cheng Li
l7501
May 14, 2008 10:37 pm
Lene, This is the latest dChip: http://biosun1.harvard.edu/~cli/dchip.exe [V12/14/07+] <http://cran.r-project.org/contrib/extra/dcom/> Install R-COM (run...
2746
jai
jai75in
May 13, 2008 11:32 am
Hi Cheng, Can dCHIP perform Multiple Testing Correction e.g Benjamini and Hochberg, Bonferroni etc. I could not find them in Compare samples. Just wondering if...
2745
rasklene
May 13, 2008 8:34 am
To Dr. Li, I have recently installed dChip to analyze some array data. In addition I have installed the program R to be able to do some LDA. Installing the...
2741
Chia Chu
kakoii19
May 9, 2008 9:32 pm
I see. Thank you for your quick response. -Chia --- On Fri, 5/9/08, Cheng Li <cli@...> wrote: From: Cheng Li <cli@...> Subject: RE:...
2740
Cheng Li
l7501
May 9, 2008 8:56 pm
Chia, dChip has not been tested on making gene info file for this array. You may manually copy and paste columns to make a file. Unzip this file for a format: ...
2739
Jerry Chu
kakoii19
May 9, 2008 7:17 pm
Hi, I want to use dchip to analyze some e_coli_2 arrays but the program shuts down due to error every time when I try to generate information files from...
2738
David Carter
dcarter442000
May 6, 2008 1:38 pm
Hello Marsha, You can make the gene info file within dChip using the Affy porcine annotations .csv. I made them 2 years ago with no problem. Look under ...
2737
daughterofthedancinga...
daughterofth...
May 5, 2008 8:50 pm
Hello, Can you tell me if gene info files are available for the pig? I've tried looking for them on Affymetrix's site to no avail. Thanks! Marsha C....
2736
Cheng Li
l7501
May 3, 2008 12:34 am
Carol, You can try checking "Combine comparisons/output expression values". Cheng Li _____ From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf...
2735
mothersquid
May 3, 2008 12:17 am
Hello, I recently replaced my dCHIP2005 with the latest download from the website. My compare_result files with the old version would show probeset expression...
2734
Cheng Li
l7501
May 2, 2008 12:09 am
Please post dChip error messages. CL ... file, ... 5.0...
Dear Dr Li: I can visualize and analyze each 250k array set but I don't arrive to combine 250k Nsp and Sty arrays. Please, could you to indicate me how to...
2732
jishan561109
Apr 27, 2008 5:21 pm
Hi, Can someone help me to analyze CN and LOH using dChip from SNP 5.0 array data. I need to know detail infoamtion regarding the the necessary files for...
2731
jishan561109
Apr 26, 2008 11:41 pm
Dr. Li, Which CDF file should I use for dChip copy number and LOh studies. BTW, Have you updated you dChip user manual recently? the latest on I found is 2005...
2730
ccyen328.tw
Apr 26, 2008 2:23 pm
Dear Dr. Li: Is it possible that you can given dChip a function to set an uneven range of CN in LOH? Such as 2-0.335~2+10. In this way we can encompass both...
2729
Cheng Li
l7501
Apr 24, 2008 8:21 pm
Hello everyone, I am pleased to announce that we are partnering with Bioinformatics.Org to do an online workshop on dChip using web conferencing technology. ...
2727
Cheng Li
l7501
May 24, 2007 1:44 am
Dear all, To better support the dChip software usage, we will switch to a forum to discuss dChip: http://dchip.forum5.com/. You can log into this forum and...
2714
Zhang, Jacob
depspace
May 14, 2007 7:25 pm
Dear Dchipper: I am using dchip to study a family pedigree using 10K SNP chip data. Here is my question. Each time I run the Merlin, it only analyze a specific...
2707
Cheng Li
l7501
May 4, 2007 12:14 am
Corina, Since this is SNP array, probably you should not use P call % in filtering. Cheng ... From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On...
2706
Corina Shtir
cshtir
May 3, 2007 9:53 pm
Dear Cheng, I am quite new at running DChipSNP, and have a basic question; when I am trying to filter genes in preparation of gene clustering analysis (for now...
2702
Cheng Li
l7501
May 1, 2007 11:13 pm
Martin, You can check if the external data file is saved in txt format. dChip manual has links to CDF files: ...
2701
mengmin liu
liumengmin
May 1, 2007 10:43 pm
Hi, Dr. Li I would like to combine two different groups of dchip data which were separately normalized and model based-expression using normal control. I would...
2700
Martin Strand
martinstrand
May 1, 2007 10:27 pm
The GO files i used was downloaded via the link from your page, but it works if i do not spesify the GO files. However, when I have the gene info file and try...
2699
Cheng Li
l7501
May 1, 2007 5:35 pm
Rich, This updated dchip (5/1) can also provide more error information to help determine what cdf file is needed: Http://biosun1.harvard.edu/~cli/dchip2006.exe...
2698
Richard Friedman
friedman@...
May 1, 2007 2:37 pm
... David, I am using 10k chips. I have tried it with both "PM only" checked and unchecked. I believe that the log below shows that I am in the right working ...
2696
Richard Friedman
friedman@...
Apr 30, 2007 9:58 pm
Dear Cheng and other dChip users: I am trying to use dChip for copy number and I am unable to read the cel files. A worf file with a record of my run and a...
2695
huangym128
Apr 28, 2007 8:27 pm
Dear Sir: Yes,I come across the similiar but much more serious problem. I use dChip to analysis my 500K SNP dchip genetyping results in a family with autosome...
2694
Cheng Li
l7501
Apr 28, 2007 12:59 am
This may be a bug to handle the latest GO files. You may try these recent gene info files here instead: ...
2693
martinstrand
Apr 27, 2007 1:13 pm
I have the same problem, the GO files are read, but when parsing the NetAffx CSV there is an error where a term is not found. I use the latest files from...
