[BioC] Annotating Results for HuEx 1.0 STv2 - Oligo
Atul
atulkakrana at outlook.com
Thu Aug 29 05:40:55 CEST 2013
Hi All,
I am using Oligo package to analyse samples generated using HuEx 1.0 ST
v2 chip. The problem I am facing is with annotating the results.
Here is my code (simplified):
celFilesA <- list.celfiles()
AF_data.A <- read.celfiles(celFilesA,pkgname='pd.huex.1.0.st.v2')
AF.eset.RMA <- rma(AF_data.A,target='core')
> dim(exprs(AF.eset.RMA))
[1] 22011 10
##Attempt to annotate
library(biomaRt)
ID <- rownames(AF.eset.RMA)
ensembl <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl')
Anno <-
getBM(attributes=c("strand","transcript_start","chromosome_name","hgnc_symbol"),filters=c("affy_huex_1_0_st_v2"),values=ID,mart=ensembl)
> dim(Anno)
[1] 1635 4
As you see, out of total 22011 genes/probeset I can annotate only 1635
genes/probesets. Is there any way I can get the annotations for all of
the genes/probesets and add them back to my expression set
(AF.eset.RMA). So, that annotations are included in the final results.
Usually, with other chips I do this:
ID <- featureNames(AF.eset.RMA)
Symbol <- getSYMBOL(ID, 'mouse4302.db')
Name <- as.character(lookUp(ID, "mouse4302.db", "GENENAME"))
tmp <- data.frame(ID=ID, Symbol=Symbol, Name=Name,stringsAsFactors=F)
tmp[tmp=="NA"] <- NA
fData(AF.esetRMA) <- tmp
And this is what I want to achieve in present case. I would appreciate
your help.
Thanks
AK
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