[BioC] Puma question
Richard Pearson
richard.pearson at well.ox.ac.uk
Thu Oct 14 18:28:15 CEST 2010
Hi Marco
My guess is that there is a problem with your targets.csv file. It seems that your "adf" object has no varMetadata:
varLabels and varMetadata description:
X.Group.:
X.Treatment.:
To confirm this is not a problem specifically with puma, could you try a different summarisation method on your AffyBatch object, e.g. what do you get
if you try:
rma(Data)
If you'd like to send your targets.csv file to me I could have a quick look to see if I can spot the problem.
Best wishes
Richard
On 14/10/2010 10:49, Manca Marco (PATH) wrote:
>
>
> Dear BioC members,
>
> I'm trying to perform an analysis of set of mouse microarrays (Affymetrix Mouse Gene 1.0-ST Array Transcriptcluster) using the package puma. I'm quite new to this package so I'm trying to follow the vignette but I'm getting stuck with a very early error that I'm unable to interpret and tackle:
>
>> Data.mmgmos<- mmgmos(Data)
> Error in exprs(object)[mmIndex, ]<- value :
> NAs are not allowed in subscripted assignments
>
> Following I'm attaching my whole commands' sequence, and sessionInfo, for your convenience
>
>
>> library("affy", "mogene10stv1.r3cdf")
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
>> getwd();
> [1] "/home/..."
>> workingDir = "/home/...";
>> setwd(workingDir);
>> #loading the data
>> Data<-read.affybatch("02_(MoGene-1_0-st-v1).CEL","07_(MoGene-1_0-st-v1).CEL","08_(MoGene-1_0-st-v1).CEL","09_(MoGene-1_0-st-v1).CEL","10_(MoGene-1_0-st-v1).CEL","11_(MoGene-1_0-st-v1).CEL","13_(MoGene-1_0-st-v1).CEL","18_(MoGene-1_0-st-v1).CEL","20_(MoGene-1_0-st-v1).CEL","23_(MoGene-1_0-st-v1).CEL","30_(MoGene-1_0-st-v1).CEL","31_(MoGene-1_0-st-v1).CEL", cdfname = "mogene10stv1.r3cdf")
> Warning message:
> In read.affybatch("02_(MoGene-1_0-st-v1).CEL", "07_(MoGene-1_0-st-v1).CEL", :
> Incompatible phenoData object. Created a new one.
>
>> annotation(Data) = "mogene10sttranscriptcluster.db"
>> Data
> AffyBatch object
> size of arrays=1050x1050 features (21 kb)
> cdf=mogene10stv1.r3cdf (34760 affyids)
> number of samples=12
> number of genes=34760
> annotation=mogene10sttranscriptcluster.db
> notes=
>> adf<- read.AnnotatedDataFrame("targets.csv",header=TRUE, sep="\t")
>> adf
> An object of class "AnnotatedDataFrame"
> rowNames: "02_(MoGene-1_0-st-v1).CEL", "07_(MoGe
> ne-1_0-st-v1).CEL", ..., "08_(MoGene-1_0-st-v1).CEL" (12 total)
> varLabels and varMetadata description:
> X.Group.:
> X.Treatment.:
>> phenoData(Data)<-adf
>> library("puma")
>> Data.mmgmos<- mmgmos(Data)
> Error in exprs(object)[mmIndex, ]<- value :
> NAs are not allowed in subscripted assignments
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-pc-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=en_US.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] puma_1.12.0 mogene10stv1.r3cdf_2.5.0 affy_1.24.2
> [4] Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.1
>
>
> Thank you in advance for your attention. Any comment or suggestion would be highly apreciated.
>
> Marco
>
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht
>
> E-mail: m.manca at maastrichtuniversity.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
>
>
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> ________________________________________
> Da: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] per conto di Sean Davis [sdavis2 at mail.nih.gov]
> Inviato: martedì 12 ottobre 2010 11.40
> A: Georgia Tsiliki
> Cc: Bioconductor Newsgroup
> Oggetto: Re: [BioC] GEOquery question
>
> On Tue, Oct 12, 2010 at 4:51 AM, Georgia Tsiliki<g_tsiliki at hotmail.com>wrote:
>
>> Dear Dr Davis,
>> I am a biostatistician at BRFAA, Athens. I am currently using the
>> 'GEOquery' package with Bioconductor/R. I had a problem with GSE3494 series;
>> particularly, i cannot download the 'Data Table of the Clinicopathological
>> variables of the Upsala cohort header description' and the 'GEO Sample
>> accession numbers and associated Patient IDs header description' files. Both
>> of them are included in the GEO accession Viewer with an option to download
>> them, but I'm not sure how i can do that via the GEOquery package. I don't
>> think there's a soft file for that particular series, do you think that
>> might be the problem?
>>
>>
> Hi, Georgia.
>
> I realized a few months ago that this GSE (and others like it) existed. I
> added a function to GEOquery to grab the GSE data tables. In the case of
> GSE3494, there are two of these data tables, so the function will return a
> list of two data.frames.
>
> gsedt = getGSEDataTables('GSE3494')
>
> Now, gsedt is a list of length 2 and holds each of the GSE data tables in
> the list. You can use getGEOSuppFiles to get the actual raw data. With the
> two pieces, it is not difficult to generate an ExpressionSet using the
> normal affy/Bioc tools.
>
> Hope that helps.
>
> Sean
>
>
>
>> Thank you very much for your time,
>> Georgia Tsiliki
>>
>
> [[alternative HTML version deleted]]
>
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--
Dr Richard D Pearson richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics http://www.well.ox.ac.uk/~rpearson
University of Oxford Tel: +44 (0)1865 617890
Roosevelt Drive Mob: +44 (0)7971 221181
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