[BioC] differential expression analysis for 1 vs 1 experiment

[Steve Lianoglou]

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