Hi,
recently I tried to use DEXSeq package to estimate the differentially incorporated exons. I had a problem when I am trying to read the files.
My pipeline is:
1. annotation_DEXSeq<-"/Users/lxz/Dropbox/protocol/3-database/human_genome/Homo_sapiens.GRCh37.65.DEXSeq.gff"
2. file_path_ALK<-"/Users/lxz/Dropbox/Lab_Resource/RNAseq/1-data-processing/10-splicing/2-DEXSeq/1-DEXSeq-results"
3. samples_DHL=data.frame(condition=c(rep("control",3),rep("treated",3)),row.names=dir(file_path_ALK,pattern="DEXSeq_DHL.txt"),stringsAsFactors=TRUE, check.names=FALSE)
> samples_DHL
condition
control01_DEXSeq_DHL.txt control
control02_DEXSeq_DHL.txt control
control03_DEXSeq_DHL.txt control
treated01_DEXSeq_DHL.txt treated
treated02_DEXSeq_DHL.txt treated
treated03_DEXSeq_DHL.txt treated
4. DHL_DEXSeq=read.HTSeqCounts(countfiles=file.path(file_path_ALK,rownames(samples_DHL)),design=samples_DHL,flattenedfile=annotation_DEXSeq)
the error message is:
"Error in order(aggregates$gene_id) :
unimplemented type 'list' in 'orderVector1"
any idea what is the problem and how to fix it?
Thanks.
R environment is listed here.
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 BiocInstaller_1.8.3
loaded via a namespace (and not attached):
[1] biomaRt_2.14.0 hwriter_1.3 RCurl_1.95-3 statmod_1.4.16 stringr_0.6.2 tools_2.15.1
[7] XML_3.95-0.1
recently I tried to use DEXSeq package to estimate the differentially incorporated exons. I had a problem when I am trying to read the files.
My pipeline is:
1. annotation_DEXSeq<-"/Users/lxz/Dropbox/protocol/3-database/human_genome/Homo_sapiens.GRCh37.65.DEXSeq.gff"
2. file_path_ALK<-"/Users/lxz/Dropbox/Lab_Resource/RNAseq/1-data-processing/10-splicing/2-DEXSeq/1-DEXSeq-results"
3. samples_DHL=data.frame(condition=c(rep("control",3),rep("treated",3)),row.names=dir(file_path_ALK,pattern="DEXSeq_DHL.txt"),stringsAsFactors=TRUE, check.names=FALSE)
> samples_DHL
condition
control01_DEXSeq_DHL.txt control
control02_DEXSeq_DHL.txt control
control03_DEXSeq_DHL.txt control
treated01_DEXSeq_DHL.txt treated
treated02_DEXSeq_DHL.txt treated
treated03_DEXSeq_DHL.txt treated
4. DHL_DEXSeq=read.HTSeqCounts(countfiles=file.path(file_path_ALK,rownames(samples_DHL)),design=samples_DHL,flattenedfile=annotation_DEXSeq)
the error message is:
"Error in order(aggregates$gene_id) :
unimplemented type 'list' in 'orderVector1"
any idea what is the problem and how to fix it?
Thanks.
R environment is listed here.
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 BiocInstaller_1.8.3
loaded via a namespace (and not attached):
[1] biomaRt_2.14.0 hwriter_1.3 RCurl_1.95-3 statmod_1.4.16 stringr_0.6.2 tools_2.15.1
[7] XML_3.95-0.1
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