[BioC] edgeR

[James W. MacDonald]

Hi Jahn,

Note that the name of the first column of your data is RefSeq, and you 
are subsetting on RefSeqID, which doesn't appear to exist.

Best,

Jim



On Tuesday, December 17, 2013 1:34:28 AM, Jahn Davik [guest] wrote:
>
> 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
>>
>
> --
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099