In your makeVectors call, it appears you are saying you only have one array
per batch and only 25 arrays total. I believe this is what is producing the
error. You need multiple arrays per batch to create frmavecs. And you
should probably use more than 25 arrays to create the frmavecs.

Best,
Matt
On Nov 10, 2011 9:10 AM, "Wang,Ying" <YWang31@mdanderson.org> wrote:

> Dear all,
>
> I have 25 cel files from Affymetrix U133AAofAv2 platform.  I need to
> quantify the data using fRMA. Since there is no available vector package
> for this platform, I have to construct one using frma Tools. Here is my
> code and the "missing value" problem when generating this vector. Any help
> will be highly appreciated. Thank you very much.
>
> > u133aaofav2frmavecs=makeVectorsAffyBatch(cel.files, 1:25,
> file.dir=celpath)
> Read in: ....
> .......
>
> Data loaded
>
> Background Corrected
>
> Normalized
>
> Beginning Probe Effect Calculation ...
>
> Finished probeset: 1000
>
> Finished probeset: 2000
>
> Finished probeset: 3000
>
> Finished probeset: 4000
>
> Finished probeset: 5000
>
> Finished probeset: 6000
>
> Finished probeset: 7000
>
> Finished probeset: 8000
>
> Finished probeset: 9000
>
> Finished probeset: 10000
>
> Finished probeset: 11000
>
> Finished probeset: 12000
>
> Finished probeset: 13000
>
> Finished probeset: 14000
>
> Finished probeset: 15000
> Finished probeset: 16000
>
> Finished probeset: 17000
>
> Finished probeset: 18000
>
> Finished probeset: 19000
>
> Finished probeset: 20000
>
> Finished probeset: 21000
>
> Finished probeset: 22000
>
> Probe Effects Calculated
>
> Probe Variances Calculated
>
> Probe Set SDs Calculated
>
> Beginning Median SE Calculation ...
>
> Error in if (any(w < 0)) { : missing value where TRUE/FALSE needed
>
>
> Best,
>
> Ying
>
>
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>
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