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hello All!
I am desperately trying to run this GO analysis on my RNAseq data(human samples).
I got stuck in creating a pwf file: I have -I guess- successfully created a DE matrix, with ENS id and 0/1 as identifier of diff-non diff expressed genes.
here is the error message I encounter
genes
0 1
19004 6715
> pwf <- nullp(genes, "hg19", "ensGene")
Loading hg19 length data...
Error in qr.R(qrx) :
could not find symbol "..." in environment of the generic function
I noticed that the ENS ids in my matrix are not into double quotes...I am not sure if it really has an effect...I have just followed the manual step by step, but I am not able to figure out why is not going through (and I am newbie in all this).
Anybody can help?!!
Manu
> sessionInfo()
R version 2.15.2 (2012-10-26)
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] goseq_1.10.0 geneLenDataBase_0.99.10 BiasedUrn_1.05 edgeR_3.0.8 limma_3.14.4 BiocInstaller_1.8.3
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.7 Biobase_2.18.0 BiocGenerics_0.4.0 biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-4.2 BSgenome_1.26.1
[8] DBI_0.2-5 GenomicFeatures_1.10.2 GenomicRanges_1.10.7 grid_2.15.2 IRanges_1.16.6 lattice_0.20-15 Matrix_1.0-12
[15] mgcv_1.7-22 nlme_3.1-108 parallel_2.15.2 RCurl_1.95-4.1 Rsamtools_1.10.2 RSQLite_0.11.2 rtracklayer_1.18.2
[22] stats4_2.15.2 tools_2.15.2 XML_3.96-1.1 zlibbioc_1.4.0
I am desperately trying to run this GO analysis on my RNAseq data(human samples).
I got stuck in creating a pwf file: I have -I guess- successfully created a DE matrix, with ENS id and 0/1 as identifier of diff-non diff expressed genes.
here is the error message I encounter
genes
0 1
19004 6715
> pwf <- nullp(genes, "hg19", "ensGene")
Loading hg19 length data...
Error in qr.R(qrx) :
could not find symbol "..." in environment of the generic function
I noticed that the ENS ids in my matrix are not into double quotes...I am not sure if it really has an effect...I have just followed the manual step by step, but I am not able to figure out why is not going through (and I am newbie in all this).
Anybody can help?!!
Manu
> sessionInfo()
R version 2.15.2 (2012-10-26)
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] goseq_1.10.0 geneLenDataBase_0.99.10 BiasedUrn_1.05 edgeR_3.0.8 limma_3.14.4 BiocInstaller_1.8.3
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.7 Biobase_2.18.0 BiocGenerics_0.4.0 biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-4.2 BSgenome_1.26.1
[8] DBI_0.2-5 GenomicFeatures_1.10.2 GenomicRanges_1.10.7 grid_2.15.2 IRanges_1.16.6 lattice_0.20-15 Matrix_1.0-12
[15] mgcv_1.7-22 nlme_3.1-108 parallel_2.15.2 RCurl_1.95-4.1 Rsamtools_1.10.2 RSQLite_0.11.2 rtracklayer_1.18.2
[22] stats4_2.15.2 tools_2.15.2 XML_3.96-1.1 zlibbioc_1.4.0
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