[BioC] frmaTools library error :: makeVectorsAffyBatch() function

[Matthew McCall]

The issue is that you are trying to estimate between-batch residual
variances with only 1 batch:
abatch.ref <- makeVectorsAffyBatch(files.ref,
rep(1,length(files.ref)), file.dir=FILED)

I'm curious why you are making your own fRMA vectors. HGU133plus2 has
pre-made frozen parameter vectors in the hgu133plus2frmavecs package,
so you could use those to preprocess your data.

Best,
Matt

On Fri, May 31, 2013 at 2:40 AM, Tae-Hoon Chung <hoontaechung at gmail.com> wrote:
> Hi, all;
>
> I encountered the following error while using makeVectorsAffyBatch()
> function in frmaTools library on 141 Affymetrix HG-U133 Plus 2 chips
> (single batch).
>
>
> abatch.ref <- makeVectorsAffyBatch(files.ref, rep(1,length(files.ref)),
> file.dir=FILED)
> 1 reading GSM493958.CEL ...instantiating an AffyBatch (intensity a
> 1354896x141 matrix)...done.
> Reading in : GSM493958.CEL
> Reading in : GSM493960.CEL
> Reading in : GSM493965.CEL
> Reading in : GSM493966.CEL
> Reading in : GSM493970.CEL
>
> …
>
> Reading in : GSM494235.CEL
> Reading in : GSM494237.CEL
> Reading in : GSM494240.CEL
> Data loaded
>
> Background Corrected
>
> Normalized
>
> Beginning Probe Effect Calculation ...
>
> Finished probeset: 1000
>
> Finished probeset: 2000
>
> Finished probeset: 3000
>
> Finished probeset: 4000
>
> …
>
> Finished probeset: 53000
>
> Finished probeset: 54000
>
> 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
>
>
> Any suggestion?
> I ran the code under following environment:
>
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hgu133plus2cdf_2.11.0 AnnotationDbi_1.20.7  frmaTools_1.10.0
> [4] frma_1.10.0           affy_1.36.1           Biobase_2.18.0
> [7] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] BiocInstaller_1.8.3   Biostrings_2.26.3     DBI_0.2-5
> [4] GenomicRanges_1.10.7  IRanges_1.16.6        MASS_7.3-23
> [7] RSQLite_0.11.2        affxparser_1.30.2     affyio_1.26.0
> [10] bit_1.1-10            codetools_0.2-8       ff_2.2-11
> [13] foreach_1.4.0         iterators_1.0.6       oligo_1.22.0
> [16] oligoClasses_1.20.0   parallel_2.15.2       preprocessCore_1.20.0
> [19] splines_2.15.2        stats4_2.15.2         tools_2.15.2
> [22] zlibbioc_1.4.0
>
> Thanks in advance,
>
> TH
>
>
> --
> Tae-Hoon Chung, PhD
>
>         [[alternative HTML version deleted]]
>
>
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-- 
Matthew N McCall, PhD
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