[BioC] Limma: import files with genes missing

Daniel Brewer daniel.brewer at icr.ac.uk
Mon Apr 14 11:56:13 CEST 2008

I am trying to use limma to import a series of bluefuse post processed
files.  This is the command I am using:

CGHraw <- read.maimages(CGHFiles,source="bluefuse",

The problem is that each of these post processed files only contain the
genes that pass the QA and so different files have different probes.  I
believe that limma finds all the common probes between the files and
then only imports for them.  I would like to do the reverse, importing
all the probes that appear in any file and setting the value where they
do not appear to NA.

Any way of doing this?

I have tried importing the files separately and then merging, but that
just uses the the probe list from the first file.


Daniel Brewer, Ph.D.
Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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