User: user31888

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user3188830
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United States
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7 months ago
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1 year, 10 months ago
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Posts by user31888

<prev • 17 results • page 1 of 2 • next >
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VIPER (Protein Activity Inference) gene expression signature format
... Can we run VIPER (described here) with gene expression signatures generated from RNASeq-based differential expression experiments (e.g. DESeq, EdgeR, ...) instead of microarray data? VIPER manual mentions "It can also take two matrixes as arguments, the first one containing the ‘test’ samples and t ...
viper aracne.networks written 7 months ago by user3188830
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GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
... Hi, Being new to R, I am following the protocol for GAGE from DESeq in the GAGE vignette, but I don't think it fits the setup of my experiment. My read count table is as follow: REF SAMP1 SAMP2 SAMP3 ENSG00000000001.6 0 1 1 4 ENSG00000000008.3 1 6 3 ...
deseq gage pathview written 7 months ago by user3188830
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Comment: C: GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
... I tried that, but it returned the same error. Anyway, I used the edgeR fork to bypass the 'exp.d' calculation and it works now. Thanks ! ...
written 9 months ago by user3188830
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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 9 months ago by user3188830 • updated 9 months ago by Luo Weijun1.4k
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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 9 months 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 16 months 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 16 months 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 16 months 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 21 months 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 21 months ago by user3188830

Latest awards to user31888

Popular Question 7 months ago, created a question with more than 1,000 views. For Pathview: *** caught segfault *** cause 'memory not mapped'
Popular Question 7 months ago, created a question with more than 1,000 views. For Pathview: *** caught segfault *** cause 'memory not mapped'

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