Hi,
I am using GEOquery. Would like to convert expression set and get the following error.
> eset<-GDS2eSet(gds3289,do.log2=TRUE)
Using locally cached version of GPL2013 found here:
/var/folders/2j/9phgnly12zxcr0mp0r_bw7rr0000gp/T//RtmpKwKryS/GPL2013.annot.gz
Error in validObject(.Object) :
invalid class “ExpressionSet” object: featureNames differ between assayData and featureData
In addition: There were 31 warnings (use warnings() to see them)
I notice indeed the the GDS probe identifier are named "ID", whereas they are referred to as "ID_REF" in the GPL file. How can I edit the GDS data so that the identifiers match?
Thanks.
O.
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R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] hugene10sttranscriptcluster.db_8.3.1 hugene10stprobeset.db_8.3.1
[3] org.Hs.eg.db_3.1.2 RSQLite_1.0.0
[5] DBI_0.3.1 hugene10stv1probe_2.16.0
[7] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.3
[9] IRanges_2.2.9 S4Vectors_0.6.6
[11] hugene10stv1cdf_2.16.0 gcrma_2.40.0
[13] GEOquery_2.34.0 ggplot2_1.0.1
[15] affy_1.46.1 Biobase_2.28.0
[17] BiocGenerics_0.14.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.1 BiocInstaller_1.18.5 plyr_1.8.3 XVector_0.8.0 bitops_1.0-6
[6] tools_3.2.1 zlibbioc_1.14.0 digest_0.6.8 preprocessCore_1.30.0 gtable_0.1.2
[11] proto_0.3-10 stringr_1.0.0 Biostrings_2.36.4 grid_3.2.1 XML_3.98-1.3
[16] reshape2_1.4.1 magrittr_1.5 scales_0.3.0 MASS_7.3-44 splines_3.2.1
[21] colorspace_1.2-6 stringi_0.5-5 RCurl_1.95-4.7 munsell_0.4.2 affyio_1.36.0
