[BioC] Puma question

Manca Marco (PATH) m.manca at maastrichtuniversity.nl
Thu Oct 14 11:29:03 CEST 2010

Dear colleague,

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
> 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:
> 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) 

 [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           

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 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


This email and any files transmitted with it are confidential and solely for the use of the intended recipient.

It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for

delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED.

If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA

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.


> Thank you very much for your time,
> Georgia Tsiliki

        [[alternative HTML version deleted]]

Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list