[BioC] differential expression- edgeR
guest at bioconductor.org
Mon Dec 23 16:50:48 CET 2013
I am new to R and edgeR. I am trying to follow to example
9. Case Study: deep-sequenced short tags from the edgeR manual.
I download the data from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM272105
by clicking the full table and then saving webpage as .txt file containing
First 4 rows as below folled by fifth which contains the tag seq and count.
#TPM = tags per million
SEQUENCE COUNT TPM
CATCGCCAGCGGGCACC 1 0.37
Now we I follow the steps of 9.3 reading data and creating the DGElist: After running
< d<- readDGE(targets, skip = 5, comment.char = "#"), I get
Error in taglist[[i]] : subscript out of bounds
Can anyone please help, how I can solve this issue.
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=en_US.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 edgeR_3.4.2 limma_3.18.7
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