[BioC] Limma background subtraction etc

[Jason Skelton]

Hi Gordon and everyone

I'm having difficulty running the background correction function in LIMMA
I'm trying to use the "minimum" option but get the following error message:

 > AR123rep6RGback <- backgroundCorrect(AR123rep6RG, method="minimum")
Error in if (any(i)) { : missing value where TRUE/FALSE needed

options "none" & "half", appear to work perfectly fine, any ideas ?
once I have "corrected" I take it this just creates another RG object ?
which can then be used in normalizeWithinArrays/normalizeBetweenArrays ?

ALSO

Has anyone used the QVALUE function from John Storey with limma ?
are then any functions in limma that support the use of QVALUE
if not do you have any suggestions as to the best way to use it with limma.
If it is somehow possible to add another column of data to the toptable 
command to display M, t, P.values, B and q.values ???

thanks for any advice

Jason

-- 
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Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919