Dear bioc list,

I am trying to analyze 24 arrays from new Affy Clariom S arrays (24x plate format). I have tried to use the oligo package to read the arrays and I have encountered the problem that I would need a "platform design package" from this type of array (something like pd.clariomsarray.1.0). I have look for it but I haven't found it.

Then I have tried to create it with pdInfoBuilder package (updated recently), but unfortunately I got the error that "AffyClariomSPDInfoPkgSeed" is not defined class (when using it in the "makePdInfoPackage" function).

Anybody knows how to read these new affy arrays?

thanks in advanced

Ricardo Gonzalo Sanz, Ph.D.
Statistics and Bioinformatics Unit (UEB)
Vall d'Hebron Research Institute (VHIR)

The AffyClariomPDInfoPkgSeed class is part of the current Bioconductor release:

> suppressMessages(library(pdInfoBuilder))
> showMethods(makePdInfoPackage)
Function: makePdInfoPackage (package pdInfoBuilder)
object="AffyClariomSPDInfoPkgSeed"
object="AffyExpressionPDInfoPkgSeed"
object="AffyHTAPDInfoPkgSeed"
object="AffyMiRNAPDInfoPkgSeed"
object="AffySNPCNVPDInfoPkgSeed"
object="AffySNPCNVPDInfoPkgSeed2"
object="AffySNPPDInfoPkgSeed"
object="AffySNPPDInfoPkgSeed2"
object="AffySTPDInfoPkgSeed"
object="AffyTilingPDInfoPkgSeed"
object="GenericPDInfoPkgSeed"
object="NgsExpressionPDInfoPkgSeed"
object="NgsTilingPDInfoPkgSeed"

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

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=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] pdInfoBuilder_1.38.0 oligo_1.38.0         Biostrings_2.42.0
 [4] XVector_0.14.0       IRanges_2.8.1        S4Vectors_0.12.0
 [7] oligoClasses_1.36.0  affxparser_1.46.0    RSQLite_1.0.0
[10] DBI_0.5-1            Biobase_2.34.0       BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] GenomicRanges_1.26.1       splines_3.3.1
 [3] zlibbioc_1.20.0            bit_1.1-12
 [5] lattice_0.20-34            foreach_1.4.3
 [7] GenomeInfoDb_1.10.1        SummarizedExperiment_1.4.0
 [9] grid_3.3.1                 ff_2.2-13
[11] iterators_1.0.8            preprocessCore_1.36.0
[13] affyio_1.44.0              Matrix_1.2-7.1
[15] codetools_0.2-15           BiocInstaller_1.24.0

So if you have the current release version, you should have no problems building a pdInfo package for that array. In fact, I just did so (for all the Human, Mouse and Rat Clariom arrays) and have submitted them. They should appear on the download server in due time (maybe a couple of days?). But then it's a holiday week in the US, so maybe next week...