[BioC] normalize.invariantset
James W. MacDonald
jmacdon at uw.edu
Mon Mar 5 14:48:04 CET 2012
Hi Ali,
On 3/4/2012 5:28 AM, Ali Mohammadian wrote:
> Dear all,
>
> Newbie Here,
>
> I have a matrix a data with genes in rows and sample in columns.
>
> # express is my expression matrix
> normalize.invariantset (expres, as.matrix (apply(expres,1,mean)))
> #gives
> Error in while ((ns.old - ns)> 50) { :
> missing value where TRUE/FALSE needed
>
> What should I do?
Since you are a newbie, I won't just say RTFM. However, that is really
what you should do. From ?normalize.invariantset:
Arguments:
abatch: an AffyBatch object.
data: a vector of intensities on a chip (to normalize to the
reference).
ref: a vector of reference intensities.
prd.td: cutoff parameter (details in the bibliographic reference).
baseline.type: specifies how to determine the baseline array.
type: a string specifying how the normalization should be applied.
See details for more.
verbose: logical indicating printing throughout the normalization.
You are using positional arguments, so the two values you are passing in
should be
1) An AffyBatch object.
2) A vector of intensities.
What you are passing in to this function appears to be neither, so
getting an error isn't that surprising.
Perhaps you could say more about what you are trying to do, as passing
an expression matrix to normalize.invariantset() doesn't make sense.
Best,
Jim
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
More information about the Bioconductor
mailing list