User: Ed Siefker
Ed Siefker • 220
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Posts by Ed Siefker
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... 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.
...
written 10 weeks ago by
Ed Siefker • 220
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... 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 ...
written 10 weeks 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 11 weeks ago by
Ed Siefker • 220
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... 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 ...
written 11 weeks ago by
Ed Siefker • 220
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... 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 ...
written 5 months ago by
Ed Siefker • 220
• updated 5 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 5 months ago by
Ed Siefker • 220
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... 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 ...
written 5 months ago by
Ed Siefker • 220
• updated 5 months ago by
James W. MacDonald ♦ 47k
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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 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 9 months ago by
Ed Siefker • 220
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... 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
...
written 9 months ago by
Ed Siefker • 220
• updated 9 months ago by
Luo Weijun • 1.4k
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