[BioC] limma - background correct method=none
Hannah at mpimp-golm.mpg.de
Mon Apr 19 12:00:27 CEST 2004
The first code and top table is with default subtract (with the file with
0's for BG, and the second top table is that obtained using
RG=backgroundCorrect(RG, method="none") on the original data.
The obvious is to double check that the .gpr files are correct, and that
you haven't mixed medians and means by mistake when replacing BG with the 0's.
A problem with these files may also explain the high NA's and missing values
in your other post. I'm not sure on the file format, but check the column
headings correspond to the correct columns. I once had such a column shift
when writing spot output to .txt files with all sorts of 'interesting' results.
The other suggestion/question is could the wt.fun=wtflags(0), be having any effect?
Try the same without this, but I'd definetely look at the source data first.
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