User: JasonL_Weirather

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Posts by JasonL_Weirather

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Comment: C: GSVA package scores are opposite on mac and windows
... Thats so much for taking a deeper look into it. I can work around through executing the GSVA snipits in dockers for now.  GSVA is a favorite in our lab, I hope either a more clear way to reproduce the bug comes around or perhaps this will just be confined to this particular build of R.  If people ar ...
written 22 months ago by JasonL_Weirather10
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Comment: C: GSVA package scores are opposite on mac and windows
... Hi Robert, I saw there has been some changes to the way outputs are delivered. As I mentioned before I was working with the release version of Bioconductor and the eSet as well as the devel version.  The problem exists on both.  I took your advice and did a complete wipe of all packages and I did a ...
written 22 months ago by JasonL_Weirather10
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Comment: C: GSVA package scores are opposite on mac and windows
... Session info three: [57] stringi_1.1.5               XVector_0.17.1              [59] bindrcpp_0.2                RColorBrewer_1.1-2          [61] tools_3.4.2                 bit64_0.9-7                 [63] glue_1.1.1                  AnnotationDbi_1.39.3        [65] GenomicRanges_1.29.14     ...
written 22 months ago by JasonL_Weirather10
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Comment: C: GSVA package scores are opposite on mac and windows
... The session info two (sorry this forum wouldn't let me put it in one message): loaded via a namespace (and not attached): [1] Rcpp_0.12.13                lattice_0.20-35             [3] prettyunits_1.0.2           Rsamtools_1.29.1            [5] Biostrings_2.45.4           assertthat_0.2.0      ...
written 22 months ago by JasonL_Weirather10
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Comment: C: GSVA package scores are opposite on mac and windows
... The session info one: R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin16.7.0 (64-bit) Running under: macOS Sierra 10.12.6   Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /System/ ...
written 22 months ago by JasonL_Weirather10
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Comment: C: GSVA package scores are opposite on mac and windows
... Hi Robert.  Thanks for the reply, I'll post up some Session Info.  I got the same bug on both release and development versions of Bioconductor, so that doesn't seem to be the issue.  Sierra 10.12.6 is the OS version. Sorry you couldn't reproduce it. Based on a comment above implicating the SVD funct ...
written 22 months ago by JasonL_Weirather10
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GSVA package scores are opposite on mac and windows
... Just wanted to describe a bug I'm getting for the GSVA package. This little code bit should calculate a little TLR4 signaling pathway on the dataset. rm(list=ls()) library(GSVA) library(leukemiasEset) data(leukemiasEset) dat <- exprs(leukemiasEset) TLR4 = 'ENSG00000136869' MYD88 = 'ENSG0000017 ...
gsva bugs bug written 22 months ago by JasonL_Weirather10 • updated 22 months ago by Robert Castelo2.3k

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