[BioC] edgeR

[Jahn Davik [guest]]

Hi there,
I am making my way through the edgeR User's Guide. In chapter 4.4 I use the Tuch data set as follows:

rawdata<-read.delim("H:/bip1/RNAseq/Data/TableS1.txt",check.name=FALSE,stringsAsFactors=FALSE)

head(rawdata)
dim(rawdata)

# read the data
y<-DGEList(counts=rawdata[,4:9],genes=rawdata[,1:3])

str(y)
# Annotation

library(org.Hs.eg.db)

idfound <- y$genes$RefSeqID %in% mappedRkeys(org.Hs.egREFSEQ)

y<-y[idfound,]

dim(y)


According to the User's Guide the dimension of the y-matrix after removing those not having a NCBI annotation, should be 15577 x 6. However, when I use the User's Guide code, I end up with a y-matrix with dimension 0 x 6. 
I'm afraid I need help to figure out what I am doing wrong here.

Thank you.
jahn




 -- output of sessionInfo(): 

> rawdata<-read.delim("H:/bip1/RNAseq/Data/TableS1.txt",check.name=FALSE,stringsAsFactors=FALSE)
> 
> head(rawdata)
        RefSeq    Symbol NbrOfExons   8N 8T   33N 33T   51N  51T
1    NM_182502 TMPRSS11B         10 2592  3  7805 321  3372    9
2    NM_003280     TNNC1          6 1684  0  1787   7  4894  559
3    NM_152381     XIRP2         10 9915 15 10396  48 23309 7181
4    NM_022438       MAL          3 2496  2  3585 239  1596    7
5 NM_001100112      MYH2         40 4389  7  7944  16  9262 1818
6    NM_017534      MYH2         40 4402  7  7943  16  9244 1815
> dim(rawdata)
[1] 15668     9
> y<-DGEList(counts=rawdata[,4:9],genes=rawdata[,1:3])
> idfound <- y$genes$RefSeqID %in% mappedRkeys(org.Hs.egREFSEQ)
> y<-y[idfound,]
> dim(y)
[1] 0 6
> 

--
Sent via the guest posting facility at bioconductor.org.