[BioC] error in makeVectorsAffyBatch of frmaTools package

[Matthew McCall]

Ty,

This may be a version issue -- you have frmaTools_1.10.0 installed.
The latest release version is 1.12.0 and the latest devel is 1.13.0.
There should definitely be a pm method for AffyBatch objects.

Best,
Matt




On Fri, Jun 21, 2013 at 1:28 PM, Ty Thomson <tthomson at selventa.com> wrote:
> Hi Matt (or anyone else who might be able to help),
>
>
>
> I get an error when trying to run the makeVectorsAffyBatch() function in the
> frmaTools package.  I tried with an alternative cdf and I get the same
> error.  Any ideas? Thanks!
>
>
>
> Ty
>
>
>
>
>
>> require(frmaTools)
>
>> files <- dir()
>
>> x <- makeVectorsAffyBatch(files=files,
>
> + batch.id=rep(1:3,each=3))
>
> 1 reading GSM560669.CEL ...instantiating an AffyBatch (intensity a 506944x9
> matrix)...done.
>
> Reading in : GSM560669.CEL
>
> Reading in : GSM560670.CEL
>
> Reading in : GSM560672.CEL
>
> Reading in : GSM560675.CEL
>
> Reading in : GSM560693.CEL
>
> Reading in : GSM560712.CEL
>
> Reading in : GSM560716.CEL
>
> Reading in : GSM560724.CEL
>
> Reading in : GSM560725.CEL
>
> Data loaded
>
>
>
>
>
>
>
> Attaching package: ‘hgu133acdf’
>
>
>
> The following object(s) are masked from ‘package:hgu133ahsentrezgcdf’:
>
>
>
>     i2xy, xy2i
>
>
>
> Background Corrected
>
>
>
> Error in function (classes, fdef, mtable)  :
>
>   unable to find an inherited method for function ‘pm’ for signature
> ‘"AffyBatch"’
>
>
>
>>  sessionInfo()
>
> R version 2.15.2 (2012-10-26)
>
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>
>
> locale:
>
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
>
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
>
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
> other attached packages:
>
> [1] hgu133acdf_2.11.0          hgu133ahsentrezgcdf_16.0.0
> AnnotationDbi_1.20.7       frmaTools_1.10.0
>
>  [5] mclust_4.1                 SCAN.UPC_1.0.0             Biostrings_2.26.3
> IRanges_1.16.6
>
>  [9] oligo_1.22.0               oligoClasses_1.20.0        frma_1.10.0
> simpleaffy_2.34.0
>
> [13] gcrma_2.30.0               genefilter_1.40.0          affyio_1.26.0
> affy_1.36.1
>
> [17] Biobase_2.18.0             BiocGenerics_0.4.0
>
>
>
> loaded via a namespace (and not attached):
>
> [1] affxparser_1.30.2     annotate_1.36.0       BiocInstaller_1.8.3
> bit_1.1-10            codetools_0.2-8
>
>  [6] DBI_0.2-6             ff_2.2-11             foreach_1.4.0
> GenomicRanges_1.10.7  iterators_1.0.6
>
> [11] MASS_7.3-23           parallel_2.15.2       preprocessCore_1.20.0
> RSQLite_0.11.3        splines_2.15.2
>
> [16] stats4_2.15.2         survival_2.37-4       tools_2.15.2
> XML_3.96-1.1          xtable_1.7-1
>
> [21] zlibbioc_1.4.0
>
>



-- 
Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880