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Kachroo, Priyanka
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@kachroo-priyanka-4292
Last seen 10.1 years ago
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<-intraspotCorrelationMA.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