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 18 months 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 18 months 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 18 months 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 18 months 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 21 months ago by Ed Siefker220 • updated 21 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 21 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 21 months ago by Ed Siefker220 • updated 21 months ago by James W. MacDonald52k
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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 2.1 years 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 2.1 years 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 2.1 years ago by Ed Siefker220 • updated 2.1 years ago by Luo Weijun1.5k

Latest awards to Ed Siefker

Popular Question 18 months ago, created a question with more than 1,000 views. For minfi -- now what?
Popular Question 18 months ago, created a question with more than 1,000 views. For Full error messages?
Popular Question 18 months ago, created a question with more than 1,000 views. For Duplicate probes
Popular Question 18 months ago, created a question with more than 1,000 views. For Genbank accession annotation?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For topTable coefficient

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