[BioC] Discrepancy in differential expression gene list after intraspotCorrelation

[Kachroo, Priyanka]

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