'ArrayExpress' creates invalid AffyBatch objects
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Vlad thank you for pointing this out. This seems to be a problem with the "ArrayExpress" function in the eponymous package when applied to an Affymetrix dataset where CEL files are available. assayData(ab) contains the 1,004,004 x 4 matrix of probe intensities from the 4 arrays, whereas featureData(ab) is the information on the 45,101 *probe sets* that ArrayExpress provides for the Mouse430_2 chip, i.e. A-AFFY-45.adf.txt. As far as I can tell (and I think you found this too), this does not have an effect on downstream analysis (e.g. with affy::rma), since rma simply ignores the featureData. Still I think it would be nice for the "ArrayExpress" function to produce Biobase-compliant objects, so we'll see what can be done about that. Thank you and best wishes Wolfgang imir Morozov ha scritto: > Hi, > > There are the errors from object check >> validObject(ab) > Error in validObject(ab) : > invalid class "AffyBatch" object: 1: feature numbers differ between assayData and featureData > invalid class "AffyBatch" object: 2: featureNames differ between assayData and featureData >> length(featureNames(assayData(ab)) ) > [1] 1004004 >> length(featureNames(featureData(ab)) ) > [1] 45101 > i got the same error messages with another experiment. I don't known how it effect downstream analysis. ExpressionSet object looks Ok > > best > Vlad > > > >> package.version('ArrayExpress') > [1] "1.6.1" >> ab = ArrayExpress(input = "E-GEOD-2873") > trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-2873/index.html' > Content type 'text/html;charset=ISO-8859-1' length unknown > opened URL > ....... > downloaded 7951 bytes > > trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-2873/E-GEOD-2873.raw.1.zip' > Content type 'application/zip' length 19444999 bytes (18.5 Mb) > opened URL > ================================================== > downloaded 18.5 Mb > > Read 1 item > trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-2873/E-GEOD-2873.sdrf.txt' > Content type 'text/plain' length 4505 bytes > opened URL > ================================================== > downloaded 4505 bytes > > trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/A-AFFY-45/A-AFFY-45.adf.txt' > Content type 'text/plain' length 6430799 bytes (6.1 Mb) > opened URL > ================================================== > downloaded 6.1 Mb > > trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-2873/E-GEOD-2873.idf.txt' > Content type 'text/plain' length 4942 bytes > opened URL > ================================================== > downloaded 4942 bytes > > Read 50 items > > The object containing experiment E-GEOD-2873 has been built. > >> validObject(ab) > Error in validObject(ab) : > invalid class "AffyBatch" object: 1: feature numbers differ between assayData and featureData > invalid class "AffyBatch" object: 2: featureNames differ between assayData and featureData >> length(featureNames(assayData(ab)) ) > [1] 1004004 >> length(featureNames(featureData(ab)) ) > [1] 45101 >> ab > AffyBatch object > size of arrays=1002x1002 features (21998 kb) > cdf=Mouse430_2 (45101 affyids) > number of samples=4 > number of genes=45101 > annotation=mouse4302 > notes=E-GEOD-2873 > E-GEOD-2873 > organism_part > c("organism_part_comparison_design", "transcription profiling") > NULL > >> eset=mas5(ab) >> validObject(eset) > [1] TRUE > >> sessionInfo() > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] mouse4302cdf_2.5.0 ArrayExpress_1.6.1 hgu133aprobe_2.5.0 > [4] AnnotationDbi_1.8.1 hgu133acdf_2.5.0 simpleaffy_2.22.0 > [7] gcrma_2.18.1 genefilter_1.28.2 reshape_0.8.3 > [10] plyr_0.1.9 affy_1.24.2 Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 annotate_1.24.1 Biostrings_2.14.10 > [4] DBI_0.2-5 IRanges_1.4.10 limma_3.2.1 > [7] preprocessCore_1.8.0 RSQLite_0.8-1 splines_2.10.1 > [10] survival_2.35-7 XML_2.6-0 xtable_1.5-6 > > > > Vladimir Morozov > Sr. Computational Biologist > ALS Therapy Development Institute > 215 First Street, Cambridge MA, 02142 > Phone: 617-441-7242 > www.als.net<http: www.als.net=""/> > Want to help stop ALS? Become an ALS Ambassador and take action. Learn more online at www.als.net/ambassador<http: www.als.net="" ambassador=""> > > > > ******************************************************************** ******************* > The information contained in this electronic message i...{{dropped:20}}
probe probe • 692 views
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