User: bmreilly

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bmreilly0
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Posts by bmreilly

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Comment: C: DESeq2 log2FC shrink before GSEA or not?
... Yes I liked the idea of Wald stat for that reason also. Thanks for your input, very helpful! ...
written 3 months ago by bmreilly0
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Comment: C: DESeq2 log2FC shrink before GSEA or not?
... Okay thanks for the help. I guess the fact that I get unintelligible results with shrunken LFC for the later time point makes me feel that shrunken LFC with GSEA may not be appropriate when looking at more subtle changes in gene expression. I have heard fof some people on BioStars who use the sta ...
written 3 months ago by bmreilly0
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Comment: C: DESeq2 log2FC shrink before GSEA or not?
... Thanks I'll read the apeglm paper more closely. I'm actually doing a time-series where I look at the acute affects of a drug treatment and then a later time point checking for longer-lasting or sub-acute changes. Using the shrunken LFCs in the acute time point seems to work well, but for the "re ...
written 3 months ago by bmreilly0
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DESeq2 log2FC shrink before GSEA or not?
... I have RNA-seq data from several conditions where I have deteremined differentially expressed genes using DESeq2 and I'd now like to perform gene set enrichment analysis on the log2FC values from these comparisons. My question is whether I should use the shrunken log fold changes from "lfcShrink()" ...
rnaseq deseq2 gsea gene espression written 3 months ago by bmreilly0 • updated 3 months ago by Michael Love23k
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Comment: C: How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code
... Dusan, see my comment above on James' post.  There are R packages which you will likely find useful for analyzing 450k data.  See 'missMethyl' . ...
written 13 months ago by bmreilly0
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Comment: C: How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code
... James, there is some literature on using goseq for DNA methylation data, and there is in fact a Bioconductor package called 'missMethyl' which has a function called 'gometh' which was specifically developed to apply goseq methods to the illumina 450k platform.  The idea being that genes with differi ...
written 13 months ago by bmreilly0
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Comment: C: Cannot get ggbio autoplot to run successfully on R 3.2 (3.2.2 or 3.2.3)
... I just updated to bioConductor 3.2 and I am getting the exact same error.... I have R version 3.2.3 though, do you think that may have anything to do with it? ...
written 3.3 years ago by bmreilly0
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Comment: C: RnBeads cannot locate libjasper.so.1
... It turns out the problem was in fact due to the Jasper-libs package not being installed on the compute nodes I was using.  I am new to using the shared computing cluster, so I was not aware of the possibility that the compute nodes would have different software than the nodes where I was setting up ...
written 3.9 years ago by bmreilly0
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RnBeads cannot locate libjasper.so.1
... I am attempting to run RnBeads on my institutions Cluster, and I keep getting stuck at the same step yielding this error: Loading required package: doParallel /usr/bin/gs: error while loading shared libraries: libjasper.so.1: cannot open shared object file: No such file or directory Error in logge ...
rnbeads cluster gs ghostscript shared libraries written 3.9 years ago by bmreilly0
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Comment: C: Package RnBeads not available for R 3.1.2?
... Great, thanks for the tip! ...
written 3.9 years ago by bmreilly0

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Popular Question 13 months ago, created a question with more than 1,000 views. For Package RnBeads not available for R 3.1.2?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For RnBeads cannot locate libjasper.so.1

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