[BioC] Puma question
Manca Marco (PATH)
m.manca at maastrichtuniversity.nl
Thu Oct 14 11:49:35 CEST 2010
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
>
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