Hi -
I am trying to re-analyze some old data from our lab. It is direct two-color Agilent microarray data of 3 different siRNAs done in triplicate (9 samples). The siRNA samples were Cy3 and control non-targeting siRNA samples Cy5 in all 9 datasets. I am starting from the raw data that had been uploaded to GEO.
I was able to follow the limma manual and get results from that.
However, the data was originally analyzed with SAM, and I am stuck with figuring that out. I took the normalized MAList and converted to an Expression Set to use sam from siggenes. But I cannot figure out how to specify the direct two-color comparisons. I do not want to compare between the 3 siRNAs, I want to compare each group of replicates against no change (log10=0 I guess).
I have not been able to find any guidance or tutorials for this. Any suggestions are greatly appreciated.
Joe
Did you ever find a solution to this? I also found difficulty converting the limma data into an expression set, it doesn't seem capable of understanding the two channels as control and treatment. I think agilent documentation has been largely overlooked for this program.
Why don't you start a new question, explain clearly and in details your experiment and what you want to do, and what you already tried and how it failed? Asking someone who did not log in for two years doesn't seem like a good way to get help.
As an aside, not directed at you of course, but two-color microarrays without performing dye-swaps is a poor practice.
Questions regarding to limma should be asked at bioconductor support site, this information can be found on page 9 of the manual (which I assume you read before posting).