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?
> 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:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats graphics grDevices  utils datasets methods base other attached packages:  marray_1.46.0 BiocInstaller_1.18.4  limmaGUI_1.44.0 lumi_2.20.2  Biobase_2.28.0 BiocGenerics_0.14.0  limma_3.24.13