User: user31888

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user3188830
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3 years, 10 months ago
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Posts by user31888

<prev • 24 results • page 2 of 3 • next >
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GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
... I am new to R and I am sure it is a very trivial question. I am following the 'RNA-Seq Data Pathway and Gene-set Analysis Workflows' (here: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf). At steps 3 and 4 (sections 4.4 and 4.5), there is the following co ...
gage pathview written 2.8 years ago by user3188830 • updated 2.7 years ago by Luo Weijun1.5k
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Comment: C: Pathview: *** caught segfault *** cause 'memory not mapped'
... It Works ! I did both: installing libxml2 and re-installing R XML library. ...
written 2.8 years ago by user3188830
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Comment: C: Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
... No, I used the provided binaries for both versions of R I tried. ...
written 3.4 years ago by user3188830
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Comment: C: Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
... * Compiler version: g++ (GCC) 4.9.2   * I get the exact same error using g++ (GCC) 5.1.0 * or with clang version 3.3 (tags/RELEASE_33/final)​ * Same problem using R version 3.3.0 (2016-05-03) -- "Supposedly Educational"​ ...
written 3.4 years ago by user3188830
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Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
... Hi, I am trying to install 'SomaticSignatures', but the 'RGBL' dependency cannot be installed due to a compilation error I guess. When I try to install 'RGBL' I obtain the following output: > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.2 (BiocInstaller 1.20.2), ?biocL ...
somaticsignatures rgbl written 3.4 years ago by user3188830
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Comment: C: Pathview: *** caught segfault *** cause 'memory not mapped'
... I tried the exact same code with the exact same data on my laptop (Mac) and it works just fine. I also tried other datasets and always get the same results: work locally but not on the cluster. I checked that the exact same packages and R version were installed on both machines (I get the exact sa ...
written 3.8 years ago by user3188830
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Comment: C: Pathview: *** caught segfault *** cause 'memory not mapped'
... I tried the trace command you mentioned but nothing output except the error message I described in my first post. Note: * Before the error occurred, I also updated XML package. * I am running the code on a cluster (no other programs are running)  ...
written 3.8 years ago by user3188830
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Comment: C: GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set a
... Just figured it out. My version of Cuffdiff still used 'log2.fold_change' and not 'log2.FPKMy.FPKMx.' Works now, except I have a segfault problem with Pathview now. Please see https://support.bioconductor.org/p/75920/ ...
written 3.8 years ago by user3188830
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Pathview: *** caught segfault *** cause 'memory not mapped'
... I am following the GAGE pathway analysis workflow from the 'gene_exp.diff' file produced by Cuffdiff v1.3.0 (part 7.5 here) and get the following error when using path view: > pathview(gene.data = exp.fc, pathway.id = "04110", species = "hsa", same.layer=F, kegg.native = T, out.suffix=out.suff ...
pathview segfault written 3.8 years ago by user3188830 • updated 3.1 years ago by redpick1340
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GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
... I am following the GAGE pathway analysis workflow from the 'gene_exp.diff' file produced by Cuffdiff v1.3.0 (part 7.5 here) and get the following error: # Cuffdiff fork cuff.res=read.delim(file="/home/user/gene_exp.diff", sep="\t") #notice the column name special character changes. The column used ...
gage gene names cuffdiff written 3.8 years ago by user3188830 • updated 3.8 years ago by Luo Weijun1.5k

Latest awards to user31888

Popular Question 2.6 years ago, created a question with more than 1,000 views. For GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Pathview: *** caught segfault *** cause 'memory not mapped'
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Pathview: *** caught segfault *** cause 'memory not mapped'

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