Dear All,
I have few genes that I want to know are expressed or not in few tissues and conditions (microarray data). I was wondering if anyone has used affymetrix power tools to detect the signal intensities to say whether a gene is expressed in the given condition/tissue etc. I got the normalized signal intensities but I don't know what threshold to use to say a particular gene is expressed or not.
Any other way/steps to do this will also be helpful.
Thanks, RT
Hi Ido,
Do you know if there is any way to extract p-values for the present/absence calls. I could just get the P/A/M labels using the following R code. I want to add p-values to these results. Any suggestions?
Thanks, Reetu
affy.data <- ReadAffy()
data.mas5calls = mas5calls(affy.data)
data.mas5calls.calls = exprs(data.mas5calls)