[BioC] frmaTools: error with 'convertPlatform'

[Matthew McCall]

Guido,

The frma and frmaTools packages use oligo (rather than AffyBatch)
objects for the ST arrays, so what you're trying to do is a bit
outside the intended functionality. I would also caution you against
combining data from different platforms as probe behavior can change
quite a bit.

That said, we can see whether there's some simple modification that
could let you try out what you'd like. Can you figure out at what
point in the convertPlatform function the error pops up?

Best,
Matt



On Fri, Jun 1, 2012 at 8:20 AM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> Hi,
>
> I would like to use the function ‘convertPlatform’ (from the library
> frmaTools) to convert an Affybatch object from the MoGene ST v1.1 (GeneTitan
> array) format into that of the MoGene ST v1.0 format (cartridge array), but
> I run into an error. The reason that I would like to convert that Affybatch
> object is that I would like to combine 2 experiments performed on those 2
> platform so I can normalize them together.
>
>
>
> In principle the content of the arrays is the same, that is the probeSETS
> should be identical, but the design and number of probes are different: the
> v1.0 array (cartridge) is square (1050cols x 1050rows) whereas the v1.1
> array is rectangular (990cols x 1190rows). I think this may be related to
> the error I experience. Note also that I would like to use a remapped CDF.
>
>
>
> Any suggestions?
>
> Thanks,
>
> Guido
>
>
>
>
>
>> affy.data <- ReadAffy(cdfname="mogene11stv1mmentrezg")
>
>> affy.data
>
> Loading required package: AnnotationDbi
>
>
>
> AffyBatch object
>
> size of arrays=1190x990 features (25 kb)
>
> cdf=mogene11stv1mmentrezg (21225 affyids)
>
> number of samples=23
>
> number of genes=21225
>
> annotation=mogene11stv1mmentrezg
>
> notes=
>
>> object.conv <- convertPlatform(affy.data, "mogene10stv1mmentrezg")
>
> Loading required package: mogene10stv1mmentrezgprobe
>
> Loading required package: mogene11stv1mmentrezgprobe
>
>
>
>
>
> Attaching package: ‘mogene10stv1mmentrezgcdf’
>
>
>
> The following object(s) are masked from ‘package:mogene11stv1mmentrezgcdf’:
>
>
>
>     i2xy, xy2i
>
>
>
> Error in convertPlatform(affy.data, "mogene10stv1mmentrezg") :
>
>   subscript out of bounds
>
>>
>
>
>
>
>
>
>
>
>
> Some maybe relevant array characteristics:
>
>> library(affxparser)
>
>> GeneSTv1.0 <- readCelHeader("MouseTP_Brain_01_mGENE.CEL")
>
>> GeneSTv1.0
>
> $filename
>
> [1] "./MouseTP_Brain_01_mGENE.CEL"
>
>
>
> $version
>
> [1] 1
>
>
>
> $cols
>
> [1] 1050
>
>
>
> $rows
>
> [1] 1050
>
>
>
> $total
>
> [1] 1102500
>
> <<SNIP>>
>
>
>
>> GeneSTv1.1 <- readCelHeader("MouseBrain_1.CEL")
>
>> GeneSTv1.1
>
> $filename
>
> [1] "./MouseBrain_1.CEL"
>
>
>
> $version
>
> [1] 1
>
>
>
> $cols
>
> [1] 990
>
>
>
> $rows
>
> [1] 1190
>
>
>
> $total
>
> [1] 1178100
>
> <<SNIP>>
>
>
>
>> sessionInfo()
>
> R version 2.15.0 (2012-03-30)
>
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
>
>
> locale:
>
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>
>  [7] LC_PAPER=C                 LC_NAME=C
>
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
> other attached packages:
>
> [1] frmaTools_1.8.0    affy_1.34.0        Biobase_2.16.0
> BiocGenerics_0.2.0
>
>
>
> loaded via a namespace (and not attached):
>
> [1] affyio_1.24.0         BiocInstaller_1.4.4   DBI_0.2-5
>
> [4] preprocessCore_1.18.0 zlibbioc_1.2.0
>
>
>
>
>
> ---------------------------------------------------------
>
> Guido Hooiveld, PhD
>
> Nutrition, Metabolism & Genomics Group
>
> Division of Human Nutrition
>
> Wageningen University
>
> Biotechnion, Bomenweg 2
>
> NL-6703 HD Wageningen
>
> the Netherlands
>
> tel: (+)31 317 485788
>
> fax: (+)31 317 483342
>
> email:      guido.hooiveld at wur.nl
>
> internet:   http://nutrigene.4t.com
>
> http://scholar.google.com/citations?user=qFHaMnoAAAAJ
>
> http://www.researcherid.com/rid/F-4912-2010
>
>



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