
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>



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