[BioC] Discrepancy in differential expression gene list after intraspot correlation

Gordon K Smyth smyth at wehi.EDU.AU
Fri Oct 15 00:06:14 CEST 2010

Dear Priyanka,

Sorry this is causing you problems, but there's not much we can do to help 
you based on the information you give.

You say that you did an analysis a few months back, and another analysis 
more recently, and got somewhat different lists of genes.  But you don't 
tell us what the two analyses were or how they were different, except that 
at least one of them is a single channel approach.  It's not much to go 
on!  There has been no change to the limma code in the meantime, so it 
much be your analysis that has changed.

I'm guessing that your first analysis might have been a standard log-ratio 
analysis.  Of course, this will give somewhat different results to a 
single-channel analysis, especially when there is very little differential 
expression to start with.  The single-channel analysis will generally 
detect more differential expression.  When the effects are strong, the 
same genes will appear in both analyses with much the same fold changes, 
but if the effects are very weak, the single-channel analysis will pick up 
more effects and the gene order may change quite a bit.

If you still need advice, it would be best to at least give your targets 
frame so that we can see what your experimental design is.  But if the 
issue is simply that log-ratio and single-channel analyses can give 
different results, there's not much mystery about that.

Best wishes

> Date: Wed, 13 Oct 2010 10:48:12 -0500 (CDT)
> From: "Kachroo, Priyanka" <priya_coll at neo.tamu.edu>
> To: "." <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Discrepancy in differential expression gene list after
> 	intraspotCorrelation
> Dear BioC
> I am trying to perform a single channel analysis and previously ( a 
> couple of months back) did not get a warning message with 10 microarray 
> slides ( 6 diseases + 4 controls) and now when i try to re-run the 
> analysis i get the message "In remlscore(y, X, Z) : reml: Max iterations 
> exceeded" after i do this step : 
> corfit<-intraspotCorrelation(MA.Aq,design)
> I read in the previous posts that we can ignore some warning messages, 
> however if i had 30 differentially expressed genes (DE genes) in the old 
> analysis i now get 120 genes. There is not much overlap between the 
> results. And this is what concerns me.
> Experiment design
> Control ( 2 time points: Ct0 and Ct10) and Disease ( 2 time points: Dt0 and Dt10).
> I hybridized Ct0 and Ct10 ( 4 samples)  and Dt0 and Dt 10( 6 samples). 
> Now i would like to get DE genes for Dt0 versus ct0 and also Dt10 versus 
> Ct10. And so i resorted to single channel analysis. Can limma experts 
> please help me in this regard. I am a graduate student and am really 
> struggling with this problem.
> Best Regards
> Priyanka
> Graduate Assistant Research
> Texas A&M University

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