[BioC] Affystart function in Affycoretools
James W. MacDonald
jmacdon at med.umich.edu
Tue Jul 24 15:44:53 CEST 2007
Hi Sachin,
I fixed the problem and pushed to the release repository. The patched
version of affycoretools will be 1.8.1, and should appear in the next
few days.
Thanks for the bug report.
Best,
Jim
Sachin Mathur wrote:
> Dear Jim,
>
> I finally managed to get our IT to sort out the firewall issue and
> update the packages as you had indicated, but I still get the same
> error.
>
>> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
> background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...done.
> 31099 ids to be processed
> | |
> |####################|
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "se.exprs", for
> signature "ExpressionSet"
> In addition: Warning messages:
> 1: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
> 2: Incompatible phenoData object. Created a new one.
> in: read.affybatch(filenames = filenames, phenoData = phenoData)
> Execution halted
>
>> sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "splines" "tools" "stats" "graphics" "grDevices"
> "utils"
> [7] "datasets" "methods" "base"
>
> other attached packages:
> rat2302cdf affycoretools annaffy xtable gcrma
> "1.16.0" "1.8.0" "1.8.1" "1.4-6" "2.8.1"
> matchprobes biomaRt RCurl XML GOstats
> "1.8.1" "1.10.1" "0.8-0" "1.7-1" "2.2.6"
> Category Matrix lattice genefilter survival
> "2.2.3" "0.999375-0" "0.16-2" "1.14.1" "2.32"
> KEGG RBGL annotate GO graph
> "1.16.1" "1.12.0" "1.14.1" "1.16.0" "1.14.2"
> limma affy affyio Biobase
> "2.10.5" "1.14.2" "1.4.1" "1.14.1"
>
> While updating the packages, I got some warnings w.r.t. the Matrix
> package, but did not get any error messages.
>
> Regards,
> Sachin
>
>
>>>> "James W. MacDonald" <jmacdon at med.umich.edu> 7/5/2007 4:14 PM >>>
> Hi Sachin,
>
> Sachin Mathur wrote:
>> Dear Users,
>>
>> I have recently upgraded the bioconductor package to 2.0 from 1.9.
> The
>> affystart function in affycoretools used to work just fine with bioc
> 1.9
>> but I get the following errors on 2.0.
>>
>>> fnames = c("LKM1_051407.CEL","LKM2_051407.CEL")
>>> expset = affystart(fnames,plot=FALSE,pca=FALSE,express = c("mas5"))
>> background correction: mas
>> PM/MM correction : mas
>> expression values: mas
>> background correcting...done.
>> 45101 ids to be processed
>> | |
>> |####################|
>> Getting probe level data...
>> Computing p-values
>> Making P/M/A Calls
>> Error in function (classes, fdef, mtable) :
>> unable to find an inherited method for function "se.exprs",
> for
>> signature "ExpressionSet"
>> In addition: Warning messages:
>> 1: The phenoData class is deprecated, use AnnotatedDataFrame (with
>> ExpressionSet) instead
>> 2: Incompatible phenoData object. Created a new one.
>> in: read.affybatch(filenames = filenames, phenoData = phenoData)
>> Execution halted
>>
>>
>> I tried to look for se.exprs, but couldn't make any headway. Here's
> the
>> output from sessionInfo()
>>
>>> sessionInfo()
>> R version 2.5.0 (2007-04-23)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>> attached base packages:
>> [1] "splines" "tools" "stats" "graphics" "grDevices"
>> "utils"
>> [7] "datasets" "methods" "base"
>>
>> other attached packages:
>> mouse4302 mouse4302cdf affycoretools annaffy
> xtable
>> "1.16.0" "1.16.0" "1.8.0" "1.8.1"
> "1.4-6"
>> gcrma matchprobes biomaRt RCurl
> XML
>> "2.8.1" "1.8.1" "1.10.0" "0.8-0"
> "1.7-1"
>> limma affy affyio GOstats
> Category
>> "2.10.5" "1.14.1" "1.4.0" "2.2.6"
> "2.2.3"
>> Matrix lattice genefilter survival
> KEGG
>> "0.99875-2" "0.15-4" "1.14.1" "2.31"
> "1.16.1"
>> RBGL annotate Biobase GO
> graph
>> "1.12.0" "1.14.1" "1.14.0" "1.16.0"
> "1.14.2"
>
> Looks like mismatched versions. Both affy and affycoretools are old. I
>
> would update:
>
> biocLite("Biobase")
> library(Biobase)
> repos <- biocReposList()
> update.packages(repos=repos, ask=FALSE)
>
> Best,
>
> Jim
>
>
>> Thanks for the help,
>>
>> Sachin Mathur
>> 2027 Kansas Life Sciences Innovations Center
>> 3901 Rainbow Blvd.
>> Kansas City, KS 66160-7401
>> Phone: (913) 588-5966
>> Fax: (913) 588-5677
>> smathur at kumc.edu
>>
>> _______________________________________________
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>
>
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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