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Question: An error in RNA-Seq workflow at the gene level
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gravatar for zhangxiaoping403
2.3 years ago by
United States
zhangxiaoping4030 wrote:

Hello,
I'm following the RNA-seq workflow : gene-level exploratory analysis and differential expression.

in this step, the error appear,

> library("GenomicFeatures")

> gtffile <- file.path(dir,"Homo_sapiens.GRCh37.75_subset.gtf")
> txdb <- makeTranscriptDbFromGFF(gtffile, format="gtf")
Error in nchar(attrs) : 
  could not find symbol "keepNA" in environment of the generic function
In addition: Warning message:
'makeTranscriptDbFromGFF' is deprecated.
Use 'makeTxDbFromGFF' instead.
See help("Deprecated") 
> txdb <- makeTxDbFromGFF(gtffile, format="gtf")
Error in nchar(attrs) : 
  could not find symbol "keepNA" in environment of the generic function.

  I am a newcomer trying to analysis RNASeq data. Can someone help please!

 

ADD COMMENTlink modified 2.3 years ago by Martin Morgan ♦♦ 20k • written 2.3 years ago by zhangxiaoping4030
0
gravatar for Martin Morgan
2.3 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

See C: could not find symbol "keepNA" in environment of the generic function, but I think you should be able to solve this with biocLite("S4Vectors"), which will install version 0.6.2. If not, please provide the output of sessionInfo() after the error occurs.

ADD COMMENTlink written 2.3 years ago by Martin Morgan ♦♦ 20k

Thanks for your help. Updating to R-3.2.1 solves the problem

 
ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by zhangxiaoping4030
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