Entering edit mode
1) I am new to limma and to R
2) I would like to subtract the mean background from each sample individually. I don't know how to do this with limma and maintain the same object class.
3) I can export the RGlist to a spreadsheet and do this manually pretty easily I think, but how can I import the file back into limma and keep the same object class?
Thank you
> sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices [5] utils datasets methods base other attached packages: [1] marray_1.46.0 BiocInstaller_1.18.4 [3] limmaGUI_1.44.0 lumi_2.20.2 [5] Biobase_2.28.0 BiocGenerics_0.14.0 [7] limma_3.24.13
Have you read the limma User's Guide? Background correcting is part of the sample processing and there are multiple methods implemented for that.
While you can quite easily export things and then stuff them back into the object, that is sort of like taking the gas tank out of your car, putting it into the back of your truck, driving down to the station, filling up with gas, going back home and re-installing the gas tank. Or you could just drive the car there.