Dear All, I have data without replicates. So, I have a single file for condition and a single file for control. I know doing a differential analysis will not make any sense statistically. But, I was still interested as a biologist to figure this out. Any suggestion to how I should go ahead with the same?. I usually use affy package and limma for my analysis but I don't think limma works for one vs one comparison. Kindly let me know of any strategy or other tools or software that could be useful for doing the same. Thanks in advance. Himanshu [[alternative HTML version deleted]]

Hi, On Wed, Jan 23, 2013 at 6:31 PM, Himanshu Sharma <hsharm03 at="" students.poly.edu=""> wrote: > Dear All, > I have data without replicates. So, I have a single file for condition and a single file for control. I know doing a differential analysis will not make any sense statistically. But, I was still interested as a biologist to figure this out. Any suggestion to how I should go ahead with the same?. > I usually use affy package and limma for my analysis but I don't think limma works for one vs one comparison. > > Kindly let me know of any strategy or other tools or software that could be useful for doing the same. > Thanks in advance. (1) RMA normalize (2) get the `exprs()` (3) Calculate the log fold change between your two samples (4) look at genes/probes with highest abs() of value from step 3 (5) Verify any claims from step 4 with an independent assay. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact