User: Ed Siefker

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Ed Siefker200
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Posts by Ed Siefker

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Comment: C: EBcoexpress missing value where TRUE/FALSE needed
... > sessionInfo() R version 3.4.2 (2017-09-28) Platform: amd64-portbld-freebsd10.3 (64-bit) Running under: FreeBSD bio 10.3-STABLE FreeBSD 10.3-STABLE #0 r295946=5327704(9.10-STABLE): Wed Aug 3 12:13:26 PDT 2016 root@build.ixsystems.com:/tank/home/nightlies/build-freenas9/_BE/objs/tank/home/n ...
written 10 days ago by Ed Siefker200
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EBcoexpress missing value where TRUE/FALSE needed
... I have a normalized count table output from DESeq.  I ran it through varFilter(), extracted the exprs(), and converted it to a matrix with numeric values.  > head(count.matrix) S154 BE36 BA44 BI50 BE88 BE8 Sox17 27 39 56 34 57 33 Mrpl15 271 450 565 297 540 572 Lypla1 ...
software error written 10 days ago by Ed Siefker200
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lapply query MotifDb
... What's going on here?  > ETVs<-list("ETV1","ETV4", "ETV5") > query(MotifDb, ETVs[[1]]) MotifDb object of length 1 | Created from downloaded public sources: 2013-Aug-30 | 1 position frequency matrices from 1 source: |          jolma2013:    1 | 1 organism/s |           Hsapiens:    1 Hsapie ...
software error written 12 days ago by Ed Siefker200 • updated 12 days ago by Martin Morgan ♦♦ 20k
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Comment: C: assayData: 0 features
... How do I tell from the GEO website whether count data is directly available through GEOquery? ...
written 2.1 years ago by Ed Siefker200
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assayData: 0 features
... Using GEOquery, I'm not getting any features and a lot of the methods don't work.  What am I doing wrong? > gse <- getGEO("GSE48206") ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE48nnn/GSE48206/matrix/ Found 1 file(s) GSE48206_series_matrix.txt.gz   % Total    % Received % Xferd  Average Speed    ...
geoquery written 2.1 years ago by Ed Siefker200 • updated 2.1 years ago by James W. MacDonald44k
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Comment: C: multiple annotations with get()?
... Thanks, I figured the answer would be something trivial but nonobvious like that. Out of curiosity, is there a reason get() isn't designed to "do the right thing" if passed a character vector of length >1? On Fri, Oct 11, 2013 at 2:34 PM, Sean Davis wrote: > On Fri, Oct 11, 2013 at 3:31 PM, ...
written 4.0 years ago by Ed Siefker200
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multiple annotations with get()?
... I have a list of gene symbols I want to convert into entrez ids. For example, I have a txt file with these symbols: SFRP2 MGP COL10A1 MSRB3 I've loaded Biobase, annotate, and org.Hs.eg.db and done the following: symb<- read.table("example.txt",stringsAsFactors=FALSE) > get(symb, org.Hs.egSY ...
biobase annotate convert written 4.0 years ago by Ed Siefker200 • updated 4.0 years ago by Sean Davis20k
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Genbank accession annotation?
... What package would I need to transform Genbank accession numbers into gene symbols or entrez gene ids? e.g.If I search "R28020" on NCBI, it tells me that "This EST is one of 1366 sequences matched to RAB2A: RAB2A, member RAS oncogene family. " Is there a metadata package that has this kind of info ...
written 4.1 years ago by Ed Siefker200 • updated 4.1 years ago by James W. MacDonald44k
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topTable coefficient
... What does the 'coef' argument to topTable() actually do? I know it says in the manual: column number or column name specifying which coefficient or contrast of the linear model is of interest But what does that mean mathematically? Why does specifying the coefficient alter the results of the top ...
written 4.4 years ago by Ed Siefker200 • updated 4.4 years ago by Bade310
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Answer: A: inSilicoMerging and Limma
... I think the problem is with lmFit(). The merged eset definitely contain different data for each samples, since the MDS plot shows data points scattered around the origin. But after feeding this eset to lmFit(), here's what I get: ***************************************************** > fit An o ...
written 4.4 years ago by Ed Siefker200

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For topTable coefficient

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