Entering edit mode
Mark Baumeister
▴
40
@mark-baumeister-4972
Last seen 10.1 years ago
Hi all,
I am trying to convert RMA normalized intensity values in my matrix
(generated from Affymetirx raw .CEL data composed of
~30 tumor samples and 7 normal samples) to log ratios in which the
intensity values from each tumor sample are compared with a reference
sample (in this case I chose one of my normals). I was told that I
could
use a function like
> log(eset/esetRef,2)
to generate the new matrix containing log ratios.
I have reduced my data using a general filter to remove low signal and
low
variance:
> dim(esetSubNat)
[1] 1470 36
> dim(esetSubRef)
[1] 1470 1
When I try this log function I get the following error:
> esetSubLog <- log(esetSubNat/esetSubRef,2)
Error in esetSubNat/esetSubRef : non-conformable arrays
Can anyone give me any idea where I am going wrong or how else I might
try
to generate the log ratios?
Thank you,
Mark
http://sites.google.com/site/lfmmab/
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