User: Ed Siefker

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Ed Siefker220
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Posts by Ed Siefker

<prev • 48 results • page 1 of 5 • next >
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shinyTANDEM web GUI doesn't render properly
... The shinyTANDEM web interface doesn't render properly.  Here is what I see on both Firefox and Chromium on Linux. The menu bar covers up half the interface. ...
bug shinytandem written 10 weeks ago by Ed Siefker220
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Scans vs Spectra
... This is probably a pretty basic question, but what is the difference between "scans" in mzR and "spectra" in MSnbase? Why are there more scans than there are spectra?  I can plot a spectrum for every scan with plot(peaks(mz, scan)), why are so many spectra missing from my MSnExp? > mz Mass Spec ...
mass spectrometry mzr/ msnbase written 10 weeks ago by Ed Siefker220
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Answer: C: rTandem compilation failed
... For anyone else who has this problem, the solution I found was:   echo -e "CC=gcc-6\nCXX=G++-6" > ~/.R/Makevars ...
written 11 weeks ago by Ed Siefker220
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rTandem compilation failed
... Trying to install rTandem on Debian Sid.  I get this error:   g++ -I/usr/share/R/include -DNDEBUG -I"/home/hatta/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-PbieFK/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wda ...
rtandem bug compilation error written 11 weeks ago by Ed Siefker220
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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 5 months ago by Ed Siefker220 • updated 5 months 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 5 months ago by Ed Siefker220
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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 5 months ago by Ed Siefker220 • updated 5 months ago by James W. MacDonald47k
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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 9 months ago by Ed Siefker220
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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 9 months ago by Ed Siefker220
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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 9 months ago by Ed Siefker220 • updated 9 months ago by Luo Weijun1.4k

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