Comparative Marker Selection generated similar p-values

[Diana Song]

Problem: I have a microarray dataset of 23 patients, with pre and post treatment. The microarray platform is Agilent 2-color, and the data is normalized log-ratio. I'm trying to use ComparativeMakerSelection to run a DEGs analysis. The result of comparative marker selection has over 3000 significant with blocks of similar p-values.

Job ID: 

CMS - 1575990

CMSViewer - 1581382

Thank you for helping!

Best,

Diana

[Barbara Hill]

Hello Diana, 

It looks like some of our data has been deleted so I can't actually look at your jobs.

In general though, if you are seeing similar values this may mean that you need to do more stringent preprocessing.

This tutorial is a little out of date in its screenshots but the analysis remains the same and may provide some pointers for you: http://software.broadinstitute.org/cancer/software/genepattern/tutorial

Best

-Barbara