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 is ...{{dropped:21}}