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SylvainBrohée
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50
@sylvainbrohee-4860
Last seen 10.2 years ago
Dear all,
I am quite new to the "affymetrix normalization data world" and until
now, I
was always normalizing my data using the good old RMA method.
People in the wet lab I am collaborating with asked me to renormalize
a set of
data coming from different labs and I discovered the fRMA method which
is
certainly more suitable in that case.
I am working on the mouse so I used the mouse4302frmavecs package.
This is my script :
rawdata <- ReadAffy(filenames = cel.files)
eset.frma <- frma(rawdata, summarize = 'batch');
When I run this, everything seems OK (about 5-6 to run) until I run
this
command :
eset.df <- exprs(eset.frma);
which produces the following error
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "exprs", for
signature
"PLMset"
and if I look at my eset.frma object, I get this
Probe level linear model (PLMset) object
size of arrays=1002x1002
cdf=Mouse430_2 (45101 probeset ids)
number of samples=6
number of probesets=45101
number of chip level parameters for each probeset=6
annotation=mouse4302
PLMset settings
Creating function:
Preprocessing
Background Correction=Error in if
(object at model.description$preprocessing$background) { :
argument is of length zero
The only thing I'd like are the expression values of course.
Any idea about the cause of the problem?
Many thanks to all of you,
Sylvain Broh?e
