User: Ed Siefker

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Ed Siefker210
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Posts by Ed Siefker

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Comment: C: GAGE after tximport
... I figured it might be.  I wouldn't normally massage input data to get desired results.  But since I don't rightly know what gage() expects, inspecting the output for absurdity is perhaps a hint I'm doing something wrong. ...
written 10 weeks ago by Ed Siefker210
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Comment: C: GAGE after tximport
... Thanks, I reran GAGE using the counts from my dds.  This definitely changed the numbers, but didn't change the GAGE analysis > gage.data<- counts(dds2, normalized=TRUE) > E11_kegg <- gage(gage.data, gsets=kegg.gs.sym,ref=E11_ref,samp=E11_test, compare="unpaired") > E12_kegg <- ga ...
written 10 weeks ago by Ed Siefker210
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GAGE after tximport
... I have RNASeq data quantified by Salmon against the Ensembl transcriptome, and imported with tximport.  I'd like to run this through GAGE.  I have some questions. Does GAGE require normalized input?  All ?gage() says is: "   exprs: an expression matrix or matrix-like data structure, with           ...
gage tximport written 10 weeks ago by Ed Siefker210 • updated 10 weeks ago by Luo Weijun1.4k
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Comment: C: get_gene_transcript_exon_tables.pl extremely slow
... > sessionInfo() R version 3.4.2 (2017-09-28) Platform: amd64-portbld-freebsd11.0 (64-bit) Running under: FreeBSD bio 11.0-STABLE FreeBSD 11.0-STABLE #0 r321665+25fe8ba8d06(freenas/11.0-stable): Mon Sep 25 06:24:11 UTC 2017     root@gauntlet:/freenas-11-releng/freenas/_BE/objs/freenas-11-releng/fr ...
written 11 weeks ago by Ed Siefker210
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get_gene_transcript_exon_tables.pl extremely slow
... I am trying to build an up to date EnsDB following the vignette.  I have the ensembl PERL API installed. fetchTablesFromEnsembl() is running, but extremely slowly.  After about 2 hours, I have 3 meg of text files. > fetchTablesFromEnsembl(90, species = "mouse") Connecting to ensembldb.ensembl.or ...
ensembl ensembldb written 11 weeks ago by Ed Siefker210 • updated 11 weeks ago by Johannes Rainer1.1k
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Answer: A: tximport gene name
... Good point Michael. They weren't hard to find.  > tx2gene <- transcripts(EnsDb.Mmusculus.v79, columns=c("gene_name"), return.type="data.frame")[c(2,1)] > head(tx2gene,n=12)                 tx_id     gene_name 1  ENSMUST00000077235 2  ENSMUST00000179505 3  ENSMUST00000178343 4  ENSMUST00000 ...
written 11 weeks ago by Ed Siefker210
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Comment: C: tximport gene name
... I believe the "extra row" she means is the one under the column names.  71.50353 112.29713 73.64570 73.13216 60.17879 56.01880 57.25439 I did the same analysis with the same annotation this week and also have a row with no rowname.  I was worried there might be an off by one error somewhere, but my ...
written 12 weeks ago by Ed Siefker210
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DESeq2: plotCounts axis labels
... How do I adjust the size of group labels when calling plotCounts()? I've tried passing cex.axis=.5, this shrinks only the y axis. I've tried passing cex.lab=.5, this shrinks only the titles of the axes. I've tried passing cex.names, as if it were a box plot.  It doesn't work at all. ...
deseq2 graphs written 12 weeks ago by Ed Siefker210 • updated 12 weeks ago by Michael Love15k
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DESeq2, interpretation of contrasts, effect of non-contrasted conditions
... Suppose I have RNAseq data for three conditions, A, B, and C.  I can take all the data I have, build a sample table, feed it to DESeq, and use results(dds, contrast=) to compare each set of conditions. Alternatively, I can take only the data for each pairwise comparison and run DESeq for each pair. ...
deseq2 written 12 weeks ago by Ed Siefker210 • updated 12 weeks ago by Michael Love15k
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Answer: A: tximport with versioned identifiers
... Nevermind. ignoreTxVersion. Got it. ...
written 12 weeks ago by Ed Siefker210

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