Entering edit mode
Hi Daniela,
Thank you for sending the output and cdf file. It looks as though
affyPara has bug in rmaPara when a user supplies a cdf that does not
match the cdf information encoded in the cel files. The problem
appears
to be with the .initAffyBatchSF function that does initialization of
the
AffyBatch object on the workers. This function does not allow the
passing of a user supplied cdf file so the cdf used is the default
taken
from the cel files.
The cel files you are using are looking for file HuEx-1_0-st-v2 which
is
apparently in package huex10stv2cdf. The workers rmaPara spawns can't
find this package because it isn't loaded (instead we have
huex10stv2hsensecdf loaded). The workers also aren't aware that you
want
to use the huex10stv2hsensecdf package because .initAffyBatchSF does
not
pass the cdfname="huex10stv2hsensecdf" information to them. I will
contact the package maintainer about this problem and cc you on the
message.
An interim work around would be to use just.rma on the workers. Your
result will be a list of esets (one from each worker).
library(affyPara)
library(huex10stv2hsensecdf)
setwd("/home/daniela/test")
cl <- makeCluster()
# load affy on each worker so they have access to just.rma
clusterEvalQ(cl, library(affy))
eset <- clusterEvalQ(cl,
just.rma(list.celfiles(),
cdfname="huex10stv2hsensecdf"))
stopCluster(cl)
Hopefully this approach allows you to get your analysis done.
Valerie
On 10/16/2010 09:19 AM, Daniela Kamir wrote:
> Hi Valerie,
> This is Daniela (danieladna) from the Bioconductor forum. I posted
for
> help about the package affyPara.
> You asked me to send you my results.
> These are my output results:
>
>
> > library(affydata)
> > celpath <- system.file("celfiles", package="affydata")
> > fns <- list.celfiles(path=celpath,full.names=TRUE)
>
> > abatch<-ReadAffy(filenames="1031.CEL",
cdfname="huex10stv2hsensecdf")
> > abatch
>
> Attaching package: 'huex10stv2hsensecdf'
>
> The following object(s) are masked from 'package:hgu133acdf':
>
> i2xy, xy2i
>
> AffyBatch object
> size of arrays=2560x2560 features (16 kb)
> cdf=huex10stv2hsensecdf (304497 affyids)
> number of samples=1
> number of genes=304497
> annotation=huex10stv2hsensecdf
> notes=
>
> > res<-rma(abatch)
> Background correcting
> Normalizing
> Calculating Expression
> > res
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 304497 features, 1 samples
> element names: exprs
> protocolData
> sampleNames: 1031.CEL
> varLabels and varMetadata description:
> ScanDate: NA
> phenoData
> sampleNames: 1031.CEL
> varLabels and varMetadata description:
> sample: arbitrary numbering
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: huex10stv2hsensecdf
>
> But I do not manage to run just.rma:
>
> > ff<-just.rma(~/Expression-Exon/LBL__HuEx-
1_0-st-v2/Level_1/CONTROLS/TEST,cdfname="huex10stv2hsensecdf")
> Error: unexpected '/' in "ff<-just.rma(~/"
> > ff<-just.rma(/Expression-Exon/LBL__HuEx-
1_0-st-v2/Level_1/CONTROLS/TEST,cdfname="huex10stv2hsensecdf")
> Error: unexpected '/' in "ff<-just.rma(/"
> > ff<-just.rma(Expression-Exon/LBL__HuEx-
1_0-st-v2/Level_1/CONTROLS/TEST,cdfname="huex10stv2hsensecdf")
> Error: unexpected input in "ff<-just.rma(Expression-Exon/LBL__HuEx-
1_"
> > ?just.rma()
> > ff<-just.rma(abatch,cdfname="huex10stv2hsensecdf")
> Error: file names must be specified using a character vector, not a
list
> > getwd()
> [1]
> "/home/danielak/Expression-Exon/LBL__HuEx-
1_0-st-v2/Level_1/CONTROLS/TEST"
> > ff<-just.rma(home/danielak/Expression-Exon/LBL__HuEx-
1_0-st-v2/Level_1/CONTROLS/TEST,cdfname="huex10stv2hsensecdf")
> Error: unexpected input in
> "ff<-just.rma(home/danielak/Expression-Exon/LBL__HuEx-1_"
> > ff<-just.rma(/home/danielak/Expression-Exon/LBL__HuEx-
1_0-st-v2/Level_1/CONTROLS/TEST,cdfname="huex10stv2hsensecdf")
> Error: unexpected '/' in "ff<-just.rma(/"
>
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> 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=C 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] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] huex10stv2hsensecdf_12.1.0 hgu133acdf_2.6.0
> [3] affydata_1.11.10 affy_1.26.1
> [5] Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.11.1
>
> Please find attached the cdf file you asked me for. I really hope
you
> can help me find the reason why affyPara wont run or rather wont
> detect the cdf file.
> I really appreciate your help,
> Daniela
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