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User: Ed Siefker

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Ed Siefker • 220
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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 8 months ago by Ed Siefker • 220
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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 8 months ago by Ed Siefker • 220
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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 8 months ago by Ed Siefker • 220
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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 8 months ago by Ed Siefker • 220
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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 11 months ago by Ed Siefker • 220 • updated 11 months ago by jennietodd141 • 0
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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 11 months ago by Ed Siefker • 220
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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 11 months ago by Ed Siefker • 220 • updated 11 months ago by James W. MacDonald ♦ 49k
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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 15 months ago by Ed Siefker • 220
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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 15 months ago by Ed Siefker • 220
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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 15 months ago by Ed Siefker • 220 • updated 15 months ago by Luo Weijun • 1.4k

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