Tom, Thank you for this reference. It illustrates the problem nicely. In the article you say that, once identified, the data can be adjusted to remove batch...
15984
Raquel Planas
Raquel.Planas@...
Oct 28, 2004 6:33 am
Hello! I am working with pancreas total RNA as a sample, which is difficult to extract in pefect conditions (integrity). Also I am trying to find some...
15985
Gerard
vesarat.wessagowit@...
Oct 28, 2004 6:34 am
Dear Teresa I'm not sure you can normalise the data, as there are only few genes. You cannot assume that this represents normal distribution. You've got to...
Hi Jonas Collén We have been trying different labelling kits, including Amershams Post-labelling. We have used 20 micrograms total RNA as recommended in the...
I don't print super high density, but i just use regular gold seal slides and space the blots at 400um. I've never had a blank sample give a signal (i.e.,...
Hi Matt, I did use normal microscope slides with Hybond nitrocellulose membranes on top (hand made). Our setting was 1 spot on the blotting pad and 1 spots on...
15989
pragna53
pragna53@...
Oct 28, 2004 4:57 pm
Hi, I am using ease(from niaid). I tried to "update with the most recent online data", I got the following error messages. Failed to download hmlg.trip.ftp...
15990
rabatville2001
rabatville2001@...
Oct 29, 2004 6:56 am
Hello, Is there any one who can direct me to a site that has the Principal component analysis (PCA), Acctualy I would like the program that can give the 3D...
15991
STKH (Steen Krogsgaard)
GENE-ARRAYS@...
Oct 29, 2004 6:56 am
Hi Matt, we use home-made polylysine slides for prespotting and Corning GAPSII for production. The pins are conditioned by spotting ten times on these slides....
15992
Mauricio Rodriguez
mrodriguez_lanetty@...
Oct 29, 2004 6:56 am
Teresa, As Vesarat indicated before, you shouldn't use any normalization procedure which assume that most of the features (=spot=genes, etc) on the cDNA array...
15993
Tom Downey
tjd@...
Oct 29, 2004 6:57 am
Hi Teresa, You don't need to explicitly normalize for the dye effect if you use a mixed model ANOVA that includes the array as a random effect and dye as a...
15994
Kristian Almstrup
GENE-ARRAYS@...
Oct 29, 2004 6:58 am
I have been facing the same kind of problem and found that the only way to get ubiased results was to use spike in controls. Almstrup et al. 2004 Biol Reprod...
15995
Henrik Bengtsson
hb@...
Oct 29, 2004 6:58 am
Hi. One of the fundamental and classical assumptions/approximations in normalization of microarray data, especially two-color microarray data, is that most...
15996
Jeremy Clarke
jeremy.clarke@...
Oct 29, 2004 6:59 am
Hi, Genomic Solutions have been offering systems for protein microarraying for the past ten years. Our soft touch technology allows you to spot onto very ...
15997
Anna Barcelo
Anna.Barcelo@...
Oct 29, 2004 6:59 am
Hi Jonas, We always use total RNA with this Amersham kit and it works OK. The amount of RNA it depends on the organism that you are working with. For example,...
Why not do a global intensity based normalization during scanning by adjusting PMT to have a ration of intensity of both channel close to 1 !! ... genes. You...
15999
Silvia Pellegrini
GENE-ARRAYS@...
Oct 29, 2004 7:00 am
Dear Jonas, we had a very negative experience with the Cyscribe Post-labelling kit from Amersham using total RNA. Now we are using Superscript III enzyme from ...
16000
Xiuling Wang
GENE-ARRAYS@...
Oct 29, 2004 7:02 am
Hi All, Are there anyone has experience for PCR product printing? My questions are: 1. Do we need to purify PCR products after PCR experiments are done? 2. How...
Genetix offer a complete package which is specifically optimised for protein arraying. More details at http://www.genetix.com/ProteinArrayPlatform.htm Or...
16002
dstorton
dstorton@...
Oct 31, 2004 3:28 pm
The stains will give you very variable intensity results no matter what. if you use a self self CGH hyb ( make a large stock and aliquot) (i use 1ug/channel...
Hello Teresa, You have enough duplications in your sample, should be able to build a model to minimize total errors. For example to minimize: sum(i,jk) ( Aj...
16004
Tom_Volkert
GENE-ARRAYS@...
Oct 31, 2004 3:28 pm
Xiuling, You can find detailed protocols for array manufacture on our web site: http://www.whitehead.mit.edu/CMT/protocols/ArrayManuProtov1.pdf Thomas L....
Thanks to all people who have answered my question. It seems to me that a promising approach is going to be to use control and spikein spots, such as has been ...
All, Does anyone know if boiling and immediate immersion in cold water will warp codelink slides? I think our slides are getting warped during processing b/c...
16007
Atienzar Franck
Franck.Atienzar@...
Oct 31, 2004 3:28 pm
Hello, In the past, we used spike RNA as well as some house keepring genes to normalise the data with a low density array. For more details see ...
16008
mark.vanderhoek
mark.vanderhoek@...
Oct 31, 2004 3:28 pm
Plain glass works well with either DMSO or salt buffers. I don't see why the blot has to have any similar surface properties to the slide chemistry being...
16009
Todd Martinsky
todd@...
Oct 31, 2004 3:28 pm
Dear Xiuling: 1. Yes, you definitely want to use a good purification method. Contaminates in your samples can prohibit your PCR product from binding to your...
16010
David Henderson
GENE-ARRAYS@...
Oct 31, 2004 3:28 pm
... Tom is quite correct in his assessment above, but you should know that you are not restricted to using Partek. Both SAS and R (or S+) can fit this model,...
DNAjobs.com Jobs of the Week, October 29th, can be viewed online at: http://www.genesciences.com/DNAjobsNews/29Oct04.htm...
16012
Todd Martinsky
todd@...
Oct 31, 2004 3:29 pm
Good advice Steen, Staying away from materials that can act like a sponge, is good advice. The only goal of pre-printing is to remove sample from the outside...
