User: Ed Siefker

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Ed Siefker210
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Posts by Ed Siefker

<prev • 44 results • page 1 of 5 • next >
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So many unmapped probes
... I have microarray data downloaded from ArrayExpress.  The annotation is listed as "pd.hugene.1.0.st.v1".  I'm trying to annotate them with hugene10sttranscriptcluster.db.  My problem is that a large number of probes map to no symbol or refseq.  Is this normal? ``` > mydata.rma ExpressionSet (st ...
annotation hugene10sttranscriptcluster.db annotation written 6 weeks ago by Ed Siefker210 • updated 6 weeks ago by jennietodd1410
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Comment: C: AffyBatch and ArrayExpress
... I know that gcrma requires affybatch.  According to the documentation, ArrayExpress should return an affybatch. What am I missing? Is gcrma just not recommended anymore?  Is GC bias not an issue with the ST arrays?  How has that been determined? ...
written 6 weeks ago by Ed Siefker210
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AffyBatch and ArrayExpress
... I'm trying to do DEG analysis on a dataset from ArrayExpress, E-GEOD-38628.   This data is from an Affymetrix 1.0 ST array. The documentation of ArrayExpress() says:      "The output is an object of class ‘AffyBatch’ or ‘ExpressionSet’ or      ‘NChannelSet’ with the raw expression values in the as ...
affy arrayexpress bugs written 7 weeks ago by Ed Siefker210 • updated 7 weeks ago by James W. MacDonald46k
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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 5 months 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 5 months 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 5 months ago by Ed Siefker210 • updated 5 months 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 5 months 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 5 months ago by Ed Siefker210 • updated 5 months ago by Johannes Rainer1.3k
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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 5 months 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 6 months ago by Ed Siefker210

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