Moderator: James W. MacDonald

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19 hours ago
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14 years, 9 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

<prev • 4,608 results • page 1 of 461 • next >
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Answer: A: Problem with mapp ensemble protein ids to entrez ids using org.Hs.eg.db
... If you do the corresponding query in the Biomart interface at ensembl.org, you get nothing returned, so this is an issue with the Biomart server, not the biomaRt package. ...
written 19 hours ago by James W. MacDonald42k
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Comment: C: TxDb.Hsapiens.UCSC.hg19.knownGene - Error: subscript contains out-of-bounds indi
... That's most likely because you are subsetting your list using integer Entrez Gene IDs. But the names of your list aren't integers, they are character. In other words, if you do txlst[124234] you are saying 'give me the 124234th list item'. But there aren't 124,234 genes! There are like 22,000 or ...
written 1 day ago by James W. MacDonald42k
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Answer: A: Missing GenBank accession numbers in the org.Hs.egACCNUM object?
... The org.Hs.eg.db package is based on the Entrez Gene table, so by definition anything that doesn't have an Entrez Gene ID is invisible to that annotation package. Put another way, as you noted, the description for the ACCNUM table is “This object is a simple mapping of Entrez Gene identifiers https ...
written 1 day ago by James W. MacDonald42k
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Answer: A: TxDb.Hsapiens.UCSC.hg19.knownGene - Error: subscript contains out-of-bounds indi
... Entrez Gene IDs, like all other identifiers are not static. Sometimes people realize that two IDs are really pointing to the same thing, and one gets discontinued. This happens on a regular basis (monthly, I believe). The org.Hs.eg.db and TxDb.Hsapiens.UCSC.hg19.knownGene packages were built last ye ...
written 1 day ago by James W. MacDonald42k
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Answer: A: how to plot human genome chromosome Ideogram with each length by Gviz
... An alternative to Gviz that will do different length karyograms is ggbio. For an example see here. But do note that the original author of ggbio has moved on and no longer supports it, so you won't get the level of support that people get for Gviz. ...
written 2 days ago by James W. MacDonald42k
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Comment: C: Filtering genes with missing Entrez ID using "nsFilter"
... Well, what is happening is essentially this: > z <- as.data.frame(lapply(c("ENTREZID","SYMBOL"), function(x) mapIds(hugene10sttranscriptcluster.db, keys(hugene10sttranscriptcluster.db), x, "PROBEID"))) 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many map ...
written 3 days ago by James W. MacDonald42k
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Comment: C: [FIXED] Error in Gviz (actually, rtracklayer) | IdeogramTrack
... > itrack <- IdeogramTrack("chr1","hg38") > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 ...
written 3 days ago by James W. MacDonald42k
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Answer: A: Filtering genes with missing Entrez ID using "nsFilter"
... The short answer is "don't use nsFilter". I wouldn't even recommend filtering based on whether or not a probeset has an Entrez Gene ID, but that's just me. If you wanted to do something like that you could just do library(affycoretools) eset <- annotateEset(eset, hugene10sttranscriptcluster.db) ...
written 3 days ago by James W. MacDonald42k
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Comment: C: huex10stv2cdf annotation file needed
... No, unfortunately you can't normalize them together. In fact you almost surely won't be able to analyze them together either - the two arrays are just too different. If you have the same experiment that was repeated on the two platforms, then you might be able to normalize and summarize the data sep ...
written 3 days ago by James W. MacDonald42k
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Answer: A: huex10stv2cdf annotation file needed
... That's not an annotation file (which would map the probeset IDs to various gene annotations, etc). Instead that is a cdf package intended to be used with the affy package, in order to process the raw data into expression values. But do note that won't work either, as the affy package will not let y ...
written 3 days ago by James W. MacDonald42k

Latest awards to James W. MacDonald

Scholar 4 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 4 days ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Cylon 8 days ago, received 1,000 up votes.
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Why do I get different GO term sizes using the same gene universe for 2 analyses
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 16 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Scholar 24 days ago, created an answer that has been accepted. For A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
Scholar 26 days ago, created an answer that has been accepted. For A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: what is the difference between "pd.mogene.2.0.st" and "mogene20sttranscriptclust
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Concatenation of Bimap
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: featureCount - very less Successfully assigned reads
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Converting Protein Accessions Into Protein Symbols
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to deal with Affymetrix GeneChip probeids that map to multiple genes
Scholar 10 months ago, created an answer that has been accepted. For A: Converting Protein Accessions Into Protein Symbols
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: including information indicating upregulation/downregulation of genes in goana()
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: how to extract Granges not overlapping with other ganges?
Teacher 10 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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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembl
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: TopTable Problem : Unique Adj.P.Val which is near 1
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: What is logFC and "B" in methylation analysis ??

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