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@wur.nl
internet:   http://nutrigene.4t.com
http://scholar.google.com/citations?user=qFHaMnoAAAAJ
http://www.researcherid.com/rid/F-4912-2010


	[[alternative HTML version deleted]]

