[BioC] Basic ExpressionSet problems

[Sean Davis]

On Mon, Jan 14, 2013 at 11:00 AM, Forst, Christian
<christian.forst at mssm.edu> wrote:
> I have some basic problems with the ExpressionSet class of Bioconductor (as beginning user).
> For example, I do the following.
> gse40012 <- getGEO("GSE40012")
> es40012 <- gse40012[[1]]
> a40012<-addGeneInfo(es40012, annotationLibrary = "illuminaHumanv3")
>
> Now I want to export the now available annotation from the featureData (e.g `SYMBOL`)  together with the expression matrix for post-processing in a different program. How am I doing this?
>

Hi, Christian.

Something like this will do the trick.

write.table(cbind(fData(a40012)$SYMBOL,exprs(a40012)),
                file='mydata.txt',sep="\t",row.names=FALSE)

Sean


> Thanks
>     Chris
>
>
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] a4Preproc_1.6.0           illuminaHumanv3.db_1.16.0 hgu133a.db_2.8.0          org.Hs.eg.db_2.8.0        RSQLite_0.11.2
>  [6] DBI_0.2-5                 AnnotationDbi_1.20.3      limma_3.14.3              affy_1.36.0               GEOquery_2.24.0
> [11] Biobase_2.18.0            BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.26.0         AnnotationForge_1.0.3 BiocInstaller_1.8.3   IRanges_1.16.4        parallel_2.15.1
>  [6] preprocessCore_1.20.0 RCurl_1.95-3          stats4_2.15.1         tools_2.15.1          XML_3.95-0.1
> [11] zlibbioc_1.4.0
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor