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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