Moderator: James W. MacDonald

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16 years, 2 months ago
Email:
j******@u.washington.edu

I am a core member of the Bioconductor project, and I work for the University of Washington in the Department of Environmental and Occupational Health Sciences. I telecommute from Ann Arbor, MI (Go Blue!) because how will I be able to suffer the enduring pain of being a UM football fan if I can't go to the games?

Posts by James W. MacDonald

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Comment: C: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... 1.) Yes, mget is old tech as well. Use either select or mapIds. If you are just trying to annotate an ExpressionSet, you might consider using annotateEset from my affycoretools package. Why exactly are you using data.table? I can't imagine that is particularly useful in this context (where by 'this ...
written 11 hours ago by James W. MacDonald47k
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Comment: C: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... Or if you just want the RefSeq ID: select(ragene20sttranscriptcluster.db, "17610996", "REFSEQ") 'select()' returned 1:many mapping between keys and columns PROBEID REFSEQ 1 17610996 NM_019370 2 17610996 NP_062243 3 17610996 XM_008758654 4 17610996 XP_008756876   ...
written 13 hours ago by James W. MacDonald47k
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Answer: A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... The answer is a bit more complicated than what you might think. First, using the old BiMap interface (e.g., using things like ragene20sttranscriptclusterCHR directly) is probably suboptimal at this point, and you should be using either select or mapIds instead. Second, these days the ChipDb objects ...
written 13 hours ago by James W. MacDonald47k
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Answer: A: Installing GEOQuery failed with conda
... Did you see this part? ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libxml-2.0 was not found. Try installing: * deb: libxml2-dev (Debian, Ubuntu, etc) * rpm: libxml2-devel (Fedora, CentOS, RHEL) * csw: libxml2_dev (Solaris) You need the libx ...
written 16 hours ago by James W. MacDonald47k
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Answer: A: SYMBOL is not the official MGI gene symbol?
... The data for the org.Mm.eg.db package is parsed from files we download from NCBI. One of which is the gene_info.gz file. If I download that file and look for that Gene ID, this is what I get: zcat gene_info.gz | awk '{if(NR == 1 || ($1 == 10090 && $2 == 17711)) print $2"\t"$3}' GeneID Sym ...
written 17 hours ago by James W. MacDonald47k
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Comment: C: Filtering the expression values of a gene from GEO
... What exactly do you mean by 'view this classification while processing the data'? The webpage you link to shows how to use the pData function. Is there something else you want to do? ...
written 18 hours ago by James W. MacDonald47k
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Comment: C: Finding/Understanding Affy 6.0 Annotation File
... It's not a stupid question, but it is asked in a way that precludes people from being able to answer. You have 4M SNPs that you got how? The Affy 6.0 SNP array has only 900K SNP probes, but very few people would use those probes as is, but instead would impute using either the HapMap (if it was done ...
written 3 days ago by James W. MacDonald47k
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Comment: C: Problems with Organism.dplyr
... Huh. It seems a restart was all I needed for the devel issue. Sorry for the noise. > library(BiocFileCache) Loading required package: dbplyr > bfc <- BiocFileCache() ## got no tidyverse, let's wrap in as.data.frame() ;P > as.data.frame(bfcquery(bfc, "dplyr"))[,c("rid","rname"," ...
written 4 days ago by James W. MacDonald47k
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Comment: C: remove NAs values from gset
... Or probably faster naind <- is.na(rowSums(exprs(gset))) gset <- gset[!naind,] ...
written 4 days ago by James W. MacDonald47k
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Answer: A: remove NAs values from gset
... I don't believe there is a na.omit function that will dispatch correctly on an ExpressionSet, so you will need to do things slightly differently. But do note that an ExpressionSet is intended to act just like a matrix, so subsetting with the [ operator works just like you would think. naind <- ...
written 4 days ago by James W. MacDonald47k

Latest awards to James W. MacDonald

Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Best way to convert uniprot accessions to entrez gene identifiers in R
Scholar 10 weeks ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Scholar 10 weeks ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For GEOquery error
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Retrieving all genes related a go term
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: Why the log fold change of some genes returned by edgeR is not compatible with t
Scholar 3 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Voom: estimation of mean-variance relationship with gene expression data normali
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