[BioC] limma - background correct method=none

[Matthew Hannah]

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.

HTH,
Matt