Hello,
I have been running the affy package for a while now without running
into any
problems.
Now I would like to use affyPara as I have 600 .CEL files to analyze.
All my packages are up to date and all cdf files are installed.
Unfortunately affyPara cannot load any cdf files. I am not sure why.
Does anyone
have an idea how I can fix this problem?
The failure message I get is following:
Error in checkForRemoteErrors(lapply(cl, recvResult)) :
31 nodes produced errors; first error: Could not obtain CDF
environment,
problems encountered:
Specified environment does not contain HuEx-1_0-st-v2
Library - package huex10stv2cdf not installed
Bioconductor - could not connect
Calls: rmaPara -> preproPara -> clusterCall -> checkForRemoteErrors
Execution halted
I am positive that huex10stv2cdf is installed, as I have been running
it with
affy successfully from the same location.
Many thanks for your help and ideas,
Daniela
[[alternative HTML version deleted]]
On 10/08/2010 09:14 AM, danieladna wrote:
> Hello,
> I have been running the affy package for a while now without running
into any
> problems.
> Now I would like to use affyPara as I have 600 .CEL files to
analyze.
> All my packages are up to date and all cdf files are installed.
> Unfortunately affyPara cannot load any cdf files. I am not sure why.
Does anyone
> have an idea how I can fix this problem?
> The failure message I get is following:
> Error in checkForRemoteErrors(lapply(cl, recvResult)) :
> 31 nodes produced errors; first error: Could not obtain CDF
environment,
> problems encountered:
> Specified environment does not contain HuEx-1_0-st-v2
> Library - package huex10stv2cdf not installed
> Bioconductor - could not connect
> Calls: rmaPara -> preproPara -> clusterCall -> checkForRemoteErrors
> Execution halted
>
> I am positive that huex10stv2cdf is installed, as I have been
running it with
> affy successfully from the same location.
> Many thanks for your help and ideas,
> Daniela
>
>
>
Hi Daniela,
Seeing more of your code would be helpful for troubleshooting the
problem. Please provide a chunk of code that describes how you are
inputting the cdf files and what you are distributing to the nodes.
Also include the output of sessionInfo() from one of the nodes.
For example, if cl is your cluster then
clusterEvalQ(cl, sessionInfo())
I am also ccing the package maintainer on this response.
Valerie
Hi Valerie,
Unfortunately ReadAffy doesn't manage to load one file only.
I do manage to load all CEL files that are in the current location
though.
Therefore I use:
data<-ReadAffy()
data@cdfName<-"cdfname"
eset<-rma(data)
I get most of my CDF files from Brainarray.
Thanks for your help,
Daniela
[[alternative HTML version deleted]]
Hi Daniela,
On 10/14/2010 04:17 PM, danieladna wrote:
> Hi Valerie,
> Unfortunately ReadAffy doesn't manage to load one file only.
>
ReadAffy can read a single file at a time. See the examples in
?ReadAffy
then try
require(affydata)
celpath <- system.file("celfiles", package="affydata")
fns <- list.celfiles(path=celpath,full.names=TRUE)
# read a single file
abatch <- ReadAffy(filenames=fns[2])
# alternatively, read all files in a directory
abatch <- ReadAffy(celfile.path=celpath)
> I do manage to load all CEL files that are in the current location
though.
> Therefore I use:
> data<-ReadAffy()
> data at cdfName<-"cdfname"
> eset<-rma(data)
>
It is ok if you want to use all files or a single file for this
example;
a single file would simply be faster. I am interested in the output of
the example because I want to confirm that no CDF errors are thrown
when
reading a cel file with the same huex10stv2hsensecdf package you are
using in your affyPara code. I'd like to help further with this
problem
but need a couple of things from you in order to do so. Please
(1) run this code and provide the output
library(affy)
library(huex10stv2hsensecdf)
data <- ReadAffy()
data at cdfName <- "huex10stv2hsensecdf"
est <- rma(data)
(2) send me the huex10stv2hsensecdf package you are using
Thank you,
Valerie
> I get most of my CDF files from Brainarray.
> Thanks for your help,
> Daniela
>
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
Resending this message under the appropriate name for tracking
purposes.
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 won?t run or rather won?t
> > detect the cdf file.
> > I really appreciate your help,
> > Daniela
>
On 10/15/2010 04:12 PM, Valerie Obenchain wrote:
> Hi Daniela,
>
> On 10/14/2010 04:17 PM, danieladna wrote:
>
>> Hi Valerie,
>> Unfortunately ReadAffy doesn't manage to load one file only.
>>
>>
> ReadAffy can read a single file at a time. See the examples in
?ReadAffy
> then try
>
> require(affydata)
> celpath <- system.file("celfiles", package="affydata")
> fns <- list.celfiles(path=celpath,full.names=TRUE)
> # read a single file
> abatch <- ReadAffy(filenames=fns[2])
> # alternatively, read all files in a directory
> abatch <- ReadAffy(celfile.path=celpath)
>
>
>> I do manage to load all CEL files that are in the current location
though.
>> Therefore I use:
>> data<-ReadAffy()
>> data at cdfName<-"cdfname"
>> eset<-rma(data)
>>
>>
> It is ok if you want to use all files or a single file for this
example;
> a single file would simply be faster. I am interested in the output
of
> the example because I want to confirm that no CDF errors are thrown
when
> reading a cel file with the same huex10stv2hsensecdf package you are
> using in your affyPara code. I'd like to help further with this
problem
> but need a couple of things from you in order to do so. Please
>
> (1) run this code and provide the output
>
> library(affy)
> library(huex10stv2hsensecdf)
> data <- ReadAffy()
> data at cdfName <- "huex10stv2hsensecdf"
> est <- rma(data)
>
>
> (2) send me the huex10stv2hsensecdf package you are using
>
> Thank you,
> Valerie
>
>
>
>> I get most of my CDF files from Brainarray.
>> Thanks for your help,
>> Daniela
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
