Question: platform design package for new Clariom S arrays
0
gravatar for rgonzalo99
3.0 years ago by
rgonzalo990
rgonzalo990 wrote:

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)
ADD COMMENTlink modified 3.0 years ago by James W. MacDonald51k • written 3.0 years ago by rgonzalo990

I don't have experience with these new arrays (yet), but I recall a recent thread on the "D" arrays on this site:

C: Clariom D Human Microarray CDF file to package

 

Bottom line: James proves some lines of code to generate such PlatformDesign package (for the human "D" array) using the files available from Affymetrix. You say it didn't work for you, so please prove your code and session info....

ADD REPLYlink written 3.0 years ago by Guido Hooiveld2.5k
Answer: platform design package for new Clariom S arrays
1
gravatar for James W. MacDonald
3.0 years ago by
United States
James W. MacDonald51k wrote:

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...

ADD COMMENTlink written 3.0 years ago by James W. MacDonald51k

I realize that I don't have the current release version of Bioconductor. I have update it. I have already seen your pd packages on Bioconductor web page. Thank you very much!

ADD REPLYlink written 3.0 years ago by rgonzalo990
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