Moderator: James W. MacDonald

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Last seen:
3 hours ago
Joined:
15 years, 8 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 • 5,133 results • page 1 of 514 • next >
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Answer: A: Converting gene symbol list to Entrez IDs
... You are passing a data.frame to select, rather than a character vector. Presumably one of the columns of prog contains the Entrez Gene IDs, so you should subset to that column. Also note that the default of read.csv is to convert strings to factors, so you should probably include stringsAsFactors = ...
written 3 hours ago by James W. MacDonald45k
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Comment: C: Limma voom or trend?
... First, unless you are answering a question, don't use the 'Add your answer' box. Because you aren't answering a question. Use the ADD REPLY link to add replies or additional questions. I would disagree with your statement regarding clarity of the 'manual', although I am not sure what you mean by th ...
written 1 day ago by James W. MacDonald45k
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Comment: C: Problem converting annotation to GenomicRanges object
... No. The Rd files are the help pages, and wouldn't have anything to do with code functionality. I doubt this has anything to do with GenomicRanges. The error you see comes from makeGRangesFromDataFrame, which expects there to be a 'start' and 'end' column in the data.frame. If the parser in metaseqr ...
written 3 days ago by James W. MacDonald45k
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Answer: A: Fold Change and LogFC
... To answer your question requires a tautology. The difference between fold change and log fold change is in the latter case the fold change has been logged. It's not important per se; it arises because most high throughput data tends to be highly right skewed, and taking logs helps with that. ...
written 3 days ago by James W. MacDonald45k
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Answer: A: Support site search not finding posts?
... The support site search is...not good. I usually do a Google search like drnevich tximport limma-trend site:support.bioconductor.org Which brings up lots of posts that may include what you want. ...
written 5 days ago by James W. MacDonald45k
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Answer: A: DESeqDataSetFromHTSeq -- function not found
... This usually means that you haven't loaded the package that contains the function. But using the Bioconductor code search, and looking at the pdf help for both DESeq and DESeq2 indicates that this function doesn't actually exist in any Bioconductor package. Also please note that it would have been ...
written 5 days ago by James W. MacDonald45k
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Answer: A: processing agilent data by limma
... Providing stylized code that isn't really what you ran is not helpful. Unless you really have a path on your computer called /path/to/file, which would be sort of cool. As for question #1, you get an error reading in a file. Did you try reading in just that one file? How about all files but that on ...
written 5 days ago by James W. MacDonald45k
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Answer: A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
... It looks like there are three GO IDs in the org.Sc.sgd.db package that have been deprecated by the GO consortium, and you have found one of them. It's not clear how those terms got included, as for example the term you are talking about was deprecated over a year ago. > z <- unique(keys(org. ...
written 9 days ago by James W. MacDonald45k
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Answer: A: TopGO - Incorrect mapping genes to GO terms
... You are looking at the genes that have a direct mapping to that GO term, whereas topGO uses all genes that map directly to that term as well as all of its progeny.  Put another way, topGO uses GOALL, whereas you are using GO: > nrow(select(org.Mm.eg.db, "GO:1903561", "ENTREZID", "GOALL")) 'sel ...
written 11 days ago by James W. MacDonald45k
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Answer: A: GViz, different group colours
... Use the col argument. See p. 30 of the Gviz user's guide for a list of all useful arguments. ...
written 12 days ago by James W. MacDonald45k

Latest awards to James W. MacDonald

Scholar 8 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 8 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 8 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Commentator 8 months 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
Commentator 9 months 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
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 9 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 9 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 10 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 10 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 10 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 11 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 11 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 11 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 11 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 12 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 12 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?

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