[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:


   abatch: an AffyBatch object.

     data: a vector of intensities on a chip (to normalize to the

      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.



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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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