platform design package for new Clariom S arrays
1
0
Entering edit mode
rgonzalo99 • 0
@rgonzalo99-11904
Last seen 7.4 years ago

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)
oligo clariomS makeplatformdesign • 2.0k views
ADD COMMENT
0
Entering edit mode

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 REPLY
1
Entering edit mode
@james-w-macdonald-5106
Last seen 10 hours ago
United States

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 790 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6