here is the code for the issue I am having.
Thanks again for you help

>
> length(pm(data[,1]))
[1] 120855
>
>
> #############remove selected S. cerevisiae probe Ids
>
>
>
> source("RemoveProbesNew.r")
> library(yeast2cdf)
> library(yeast2probe)
> cleancdf <- cleancdfname("yeast2",addcdf=FALSE)
> ResetEnvir(cleancdf)
Loading required package: yeast2cdf
Loading required package: yeast2probe
>
> RemoveProbes(listOutProbes[1:233],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[233:467],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[467:500],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[500:600],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[600:640],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[640:650],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[650:700],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[700:710],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[710:720],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[720:800],listOutProbeSets=NULL, cleancdf)
> RemoveProbes(listOutProbes[800:884],listOutProbeSets=NULL, cleancdf)
> length(pm(data[,1]))
[1] 119991
>
>######listOutProbes is a character vector of probe ID's. I don't know why I
had to subset it like this, putting the
>######whole vector in, or larger subsets gave;
>######> RemoveProbes(listOutProbes,listOutProbeSets=NULL, cleancdf)
#######  Error in ans[[i]][, i.probes] : incorrect number of dimensions
>
>
>
>
>
>############remove s. pombe probesets
>
>
>
> s_cerevisiae<-scan("s_cerevisiae.msk", skip=2, list("", ""))
Read 5028 records
> pombe_filter_out<-s_cerevisiae[[1]]  #the probesets you DONT want.
>
>
> source("RemoveProbesNew.r")
> library(yeast2cdf)
> library(yeast2probe)
> cleancdf <- cleancdfname("yeast2",addcdf=FALSE)
> RemoveProbes(listOutProbes=NULL, pombe_filter_out, cleancdf)
> length(pm(data[,1]))
[1] 64688
?
>
>#################################read in the new data and do the RMA
>
>
> pd<-read.AnnotatedDataFrame("targets.txt",header=TRUE,row.names=1,as.is=TRUE)
# reads the names from the targets file
> data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd)  # reads all
.CEL files in the working directory and assigns them names from the target
files
>
> eset <- rma(data)#does the normalisation
Background correcting
Normalizing
Calculating Expression
Error in rma(data) : length of 'dimnames' [1] not equal to array extent
>
>
>
>
> traceback()
2: .Call("rma_c_complete", pm(object, subset), pNList, ngenes, normalize,
       background, bgversion, verbose, PACKAGE = "affy")
1: rma(data)
>
>
>
>
> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32

locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
Zealand.1252;LC_MONETARY=English_New
Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252

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

other attached packages:
 [1] yeast2probe_2.3.0   yeast2cdf_2.3.0     matchprobes_1.14.0
 [4] yeast2.db_2.2.5     RSQLite_0.7-1       DBI_0.2-4
 [7] AnnotationDbi_1.4.2 affy_1.20.0         Biobase_2.2.1
[10] limma_2.16.3

loaded via a namespace (and not attached):
[1] affyio_1.10.1        preprocessCore_1.4.0
>


Omri Yahel



On Thu, Dec 18, 2008 at 4:04 AM, Jenny Drnevich <drnevich@illinois.edu>wrote:

> Hi Omri,
>
> I'm assuming that the RemoveProbes.r function is the one I have posted to
> the Bioconductor mailing list several times, mostly recently with some
> changes on Sept 24, 2008?
> https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html
>
> If so, would you post your entire session, including the code you used to
> remove the probe sets and probes, along with your sessionInfo()? That should
> give us more details so we can help you.
>
> Thanks,
> Jenny
>
>
> At 10:08 PM 12/16/2008, Omri Yahel wrote:
>
>> Hello
>>
>> I am encountering an error during RMA of an affybatch.
>> I have used RemoveProbes.r to remove all S. pombe probesets and 864
>> individual S.cerevisiae probes from the yeast2 platform.
>>
>> >data<-ReadAffy()
>> > data
>> AffyBatch object
>> size of arrays=496x496 features (11 kb)
>> cdf=Yeast_2 (5900 affyids)
>> number of samples=26
>> number of genes=5900
>> annotation=yeast2
>> notes=
>> >
>> > length(pm(data[,1]))
>> [1] 64688
>>
>>
>> When I attempt to compute the eset
>>
>> > eset <- rma(data)
>> Background correcting
>> Normalizing
>> Calculating Expression
>> Error in rma(data) : length of 'dimnames' [1] not equal to array extent
>>
>> I assume this has something to do with the removal of individual probes
>> from
>> the environment, but am not sure and do not know how to remedy this.
>> Any help appreciated
>>
>> Omri Yahel
>> MSc student
>> School of Biological Sciences
>> University of Auckland, New Zealand
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>>
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich@illinois.edu
>

	[[alternative HTML version deleted]]

