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


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