[BioC] Error in validObject(.Object)

Surles, Monique msurles at msm.edu
Thu Jun 19 20:46:59 CEST 2014 

Thank you again for your help, Jim. I will try to do what was suggested. 

No, I didn't get the idea to read data into the AffyBatch and then add the phenoData from y'all literature. It was an error on my part.

Best,
Monique

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at uw.edu] 
Sent: Thursday, June 19, 2014 2:38 PM
To: Surles, Monique
Cc: 'bioconductor at r-project.org'
Subject: Re: [BioC] Error in validObject(.Object)

Hi Monique,

I'm cc'ing this back to the bioconductor list.

I noticed something about your code that I missed before. You shouldn't be adding the phenoData to your AffyBatch after the fact, but should be incorporating it as part of the call to ReadAffy().

In other words, you should be doing

pd <- read.table("C:/users/msurles/desktop/my info/microarray analysis/stroke/UPR/R/data analysis/analysis needed/phenodata UPR.txt", header=T, row.names=1, sep="\t")

mydata <- ReadAffy(phenoData = pd)

The reason for this is that the row.names of the phenoData should match the sampleNames of the ExpressionSet. If you look at the original email you sent, you can see that this is not the case. However, if you tell
ReadAffy() that you want to use a particular phenoData object, it will automatically order things to match.

In addition, I believe that your protocolData will end up being correct in that instance as well.

So try doing it this way and let us know if you have any further problems.

Also, where did you get the idea to read data into the AffyBatch and then add the phenoData? If that came from some of our literature, we will have to fix it.

Best,

Jim



On 6/19/2014 2:23 PM, Surles, Monique wrote:
> Thank you, Jim.  I am sorry for asking such a rookie question.
>
> Monique
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at uw.edu]
> Sent: Thursday, June 19, 2014 1:04 PM
> To: Surles, Monique; bioconductor at r-project.org
> Subject: Re: [BioC] Error in validObject(.Object)
>
> Hi Monique,
>
> If you want to put the phenoData into your AffyBatch, then you also need to add the protocolData as well. The simplest thing is to just create an empty protocolData object, and use that:
>
> protocolData(mydata) <- new("AnnotatedDataFrame", data = 
> data.frame(row.names = row.names(pData(mydata))))
>
> Best,
>
> Jim
>
>
>
> On 6/19/2014 12:38 PM, Surles, Monique wrote:
>> Hi List,
>>
>> When trying to do a RMA or Mas5 analysis on my microarray data, the following error keeps coming up....Error in validObject(.Object) :
>>     invalid class "ExpressionSet" object: sampleNames differ between phenoData and protocolDat".
>>
>> I went back and confirmed that the sample names are the same. I am using Windows 7 Professional(32 bit). Please assist... Is there something I am missing?  Your guidance is greatly appreciated.
>> Please see session information below.
>>
>> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>> Copyright (C) 2014 The R Foundation for Statistical Computing
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and 'citation()' on how to 
>> cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or 
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> source("http://www.bioconductor.org/biocLite.R")
>> Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
>>> biocLite("affy")
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0.
>> Installing package(s) 'affy'
>> trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.1/affy_1.42.2.zip'
>> Content type 'application/zip' length 2914230 bytes (2.8 Mb) opened 
>> URL downloaded 2.8 Mb
>>
>> package 'affy' successfully unpacked and MD5 sums checked
>>
>> The downloaded binary packages are in
>>
>> C:\Users\msurles\AppData\Local\Temp\RtmpI10rXE\downloaded_packages
>> Old packages: 'VariantAnnotation'
>> Update all/some/none? [a/s/n]:
>> a
>> trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.1/VariantAnnotation_1.10.3.zip'
>> Content type 'application/zip' length 3808952 bytes (3.6 Mb) opened 
>> URL downloaded 3.6 Mb
>>
>> package 'VariantAnnotation' successfully unpacked and MD5 sums 
>> checked
>>
>> The downloaded binary packages are in
>>
>> C:\Users\msurles\AppData\Local\Temp\RtmpI10rXE\downloaded_packages
>>> library(affy)
>> Loading required package: BiocGenerics Loading required package:
>> parallel
>>
>> Attaching package: 'BiocGenerics'
>>
>> The following objects are masked from 'package:parallel':
>>
>>       clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply,
>>       parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
>>
>> The following object is masked from 'package:stats':
>>
>>       xtabs
>>
>> The following objects are masked from 'package:base':
>>
>>       anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter,
>>       Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
>>       pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
>>       unique, unlist
>>
>> Loading required package: Biobase
>> Welcome to Bioconductor
>>
>>       Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
>>       'citation("Biobase")', and for packages 'citation("pkgname")'.
>>
>>> biocLite("affycoretools")
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0.
>> Installing package(s) 'affycoretools'
>> trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.1/affycoretools_1.36.1.zip'
>> Content type 'application/zip' length 1052018 bytes (1.0 Mb) opened 
>> URL downloaded 1.0 Mb
>>
>> package 'affycoretools' successfully unpacked and MD5 sums checked
>>
>> The downloaded binary packages are in
>>
>> C:\Users\msurles\AppData\Local\Temp\RtmpI10rXE\downloaded_packages
>>> library(affycoretools)
>> Loading required package: GO.db
>> Loading required package: AnnotationDbi Loading required package:
>> GenomeInfoDb Loading required package: DBI
>>
>> KernSmooth 2.23 loaded
>> Copyright M. P. Wand 1997-2009
>>
>>> biocLite("limma")
>> BioC_mirror: http://bioconductor.org
>> Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0.
>> Installing package(s) 'limma'
>> trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/windows/contrib/3.1/limma_3.20.5.zip'
>> Content type 'application/zip' length 3580258 bytes (3.4 Mb) opened 
>> URL downloaded 3.4 Mb
>>> setwd("C:/Users/msurles/desktop/my info/microarray 
>>> analysis/stroke/UPR/R/data analysis/chp files")
>>> getwd()
>> [1] "C:/Users/msurles/desktop/my info/microarray analysis/stroke/UPR/R/data analysis/chp files"
>>> mydata <- ReadAffy()#
>>> sampleNames(mydata)
>> [1] "AK02 24 hours_(HG-U133_Plus_2).CEL" "AK02 pre-occ_(HG-U133_Plus_2).CEL"  "AK06 24h post_(HG-U133_Plus_2).CEL"
>> [4] "AK51 24hours_(HG-U133_Plus_2).CEL"  "AK51 pre-occ_(HG-U133_Plus_2).CEL"  "AM14 1hour_(HG-U133_Plus_2).CEL"
>>    [7] "AM14 24hour_(HG-U133_Plus_2).CEL"   "AM14 2hour _(HG-U133_Plus_2).CEL"   "AM14 pre_(HG-U133_Plus_2).CEL"
>> [10] "Monkey 1B_(HG-U133_Plus_2).CEL"     "Monkey 2B_(HG-U133_Plus_2).CEL"     "Monkey 3B_(HG-U133_Plus_2).CEL"
>> [13] "Monkey 4B_(HG-U133_Plus_2).CEL"
>>> pData(mydata)<-read.table("C:/users/msurles/desktop/my
>>> info/microarray analysis/stroke/UPR/R/data analysis/analysis 
>>> needed/phenodata UPR.txt", header=T, row.names=1, sep="\t")
>>> pData(mydata)
>>                                    condition
>> Monkey 1B_(HG-U133_Plus_2).CEL       pre-occ
>> Monkey 2B_(HG-U133_Plus_2).CEL          1 hr
>> Monkey 3B_(HG-U133_Plus_2).CEL          2 hr
>> Monkey 4B_(HG-U133_Plus_2).CEL         24 hr
>> AM14 1hour_(HG-U133_Plus_2).CEL         1 hr
>> AM14 2hour _(HG-U133_Plus_2).CEL        2 hr
>> AM14 24hour_(HG-U133_Plus_2).CEL       24 hr
>> AM14 pre_(HG-U133_Plus_2).CEL        pre-occ
>> AK06 24h post_(HG-U133_Plus_2).CEL     24 hr
>> AK02 pre-occ_(HG-U133_Plus_2).CEL    pre-occ
>> AK02 24 hours_(HG-U133_Plus_2).CEL     24 hr
>> AK51 pre-occ_(HG-U133_Plus_2).CEL    pre-occ
>> AK51 24hours_(HG-U133_Plus_2).CEL      24 hr
>> eset <- rma(mydata)
>> Background correcting
>> Normalizing
>> Calculating Expression
>> Error in validObject(.Object) :
>>     invalid class "ExpressionSet" object: sampleNames differ between 
>> phenoData and protocolData
>>> eset1 <- mas5(mydata)
>> background correction: mas
>> PM/MM correction : mas
>> expression values: mas
>> background correcting...done.
>> 54675 ids to be processed
>> |                    |
>> |####################|
>> Error in validObject(.Object) :
>>     invalid class "ExpressionSet" object: sampleNames differ between 
>> phenoData and protocolData
>>
>>
>>
>>
>>
>> Thank you
>> Monique
>> PhD student
>>
>> 	[[alternative HTML version deleted]]
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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