User: Spollen, William G.

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Posts by Spollen, William G.

<prev • 11 results • page 1 of 2 • next >
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Answer: A: can a batch effect be determined in edgeR with only 2 reps?
... Thank you Prof. Smyth.    ...
written 3.1 years ago by Spollen, William G.30
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can a batch effect be determined in edgeR with only 2 reps?
... We have 18 treatments, in two replicates of an RNAseq experiment, for a total of 36 samples.  The first rep was generated on a HiSeq 2500 and is about 8 milllion 50 bp reads per sample.  The second rep was on a NextSeq 500, and they are 75 bp reads at ~32 million per sample.  We are following closel ...
rnaseq edger batch effect read length written 3.1 years ago by Spollen, William G.30
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Answer: A: Error installing cn.mops and Rsamtools in R 3.1.3
... I think I have discovered the problem.   When trying, and failing, to install these R packages on this cluster I used the job scheduler.  Today I tried without the scheduler and all the packages got installed (Rcpp, cn.mops, Rsamtools, cummeRbund), and the cn.mops functions that I have tried so far ...
written 4.6 years ago by Spollen, William G.30
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Answer: A: Error installing cn.mops and Rsamtools in R 3.1.3
... Gents, I think I have it solved.   I was trying to install the packages while using our LSF-like scheduler, and so R must have been looking for the compiler on one of the cluster machines, not the head node (sorry I did not state that up front. On the other cluster I use the head node and cluster n ...
written 4.6 years ago by Spollen, William G.30
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Comment: C: Error installing cn.mops and Rsamtools in R 3.1.3
... Ok, here goes: /ircf/ircfapps/src/R-3.1.3/bin/R -e "dyn.load('test.so')" R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are we ...
written 4.6 years ago by Spollen, William G.30
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Comment: C: Error installing cn.mops and Rsamtools in R 3.1.3
... Hi Martin, I do that and get exactly what you get. Bill ...
written 4.6 years ago by Spollen, William G.30
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Comment: C: Error installing cn.mops and Rsamtools in R 3.1.3
... Both produce the a.out file and both use the same g++ when run from the linux command line: $ which g++ /usr/bin/g++ $ R CMD which g++ /usr/bin/g++   ...
written 4.6 years ago by Spollen, William G.30
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Answer: A: Error installing cn.mops and Rsamtools in R 3.1.3
... Hi Nathaniel, The Rcpp did not install, as you suspected, so I will talk to the sys admin about how to access the proper C++ standard library header, or have it (re-)installed if needed.  I tried your test script, either with R CMD g++ or just g++,  and got an a.out file that is binary and does not ...
written 4.6 years ago by Spollen, William G.30
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Error installing cn.mops and Rsamtools in R 3.1.3
... Hello I am trying to install cn.mops and having trouble.  I start with a fresh install of R version 3.1.3, and then use >source("http://bioconductor.org/biocLite.R") >biocLite() to install bioconductor.  Here is the output when installing cn.mops: > biocLite("cn.mops") BioC_mirror: http:// ...
rsamtools cn.mops installation written 4.6 years ago by Spollen, William G.30
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Comment: C: EdgeR exactTest - treatment names determine sign of fold change
... Yes, I saw that. But in the context of a loop where you make the 6 pairwise comparisons of 4 group members it becomes important to name your groups in either asending or descending order to keep the fold changes consistent. I just wanted to alert anybody else in my situation to this possible source ...
written 7.6 years ago by Spollen, William G.30

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For Error installing cn.mops and Rsamtools in R 3.1.3

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