Dear Matthew,

Thanks for your reply.

I know there's a general purpose library hgu133plus2frmavecs that was
produced using microarray data from diverse tissues and batches.
However, I am interested in a specific tissue only and so don't need to
consider probes that may not be reliable in it.
So I want to know if I need my own version of normalisation parameters
based solely on data from tissue of interest or I can simply rely on
general purpose library at any rate.
I've already processed the data using the general purpose library.
And now it's the turn to develop my own version of normalisation parameters
myself and I came across the error.

In fact, I tried the procedure with artificially designated two batches.
Interestingly, it also produced an error indicating that the batches were
not of the same size (I split the sample into two batches of sizes 71 and
70, respectively).
Any suggestion?

Regards,
TH

2013년 5월 31일 금요일에 Matthew McCall<mccallm@gmail.com>님이 작성:
> 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@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
> 112 Arvine Heights
> Rochester, NY 14611
> Cell: 202-222-5880
>

-- 
Tae-Hoon Chung, PhD

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