Moderator: James W. MacDonald

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43,270
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Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
13 hours ago
Joined:
15 years, 1 month 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 • 4,872 results • page 1 of 488 • next >
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Answer: A: Computing correlation with two different data structures
... This doesn't have anything to do with any Bioconductor packages. If you just have basic questions about how to do things using R, try the R-help list (r-help@r-project.org). Or perhaps just do a google search. ...
written 13 hours ago by James W. MacDonald43k
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Answer: A: Paired t-test with 2 groups, how to I tell the DEGs between them?
... Open the limma User's Guide and search for 'interaction'. ...
written 13 hours ago by James W. MacDonald43k
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Answer: A: GEOquery problem in calling the function in Rstudio
... It appears you have lost your XML package. Does library(BiocInstaller) biocLite("XML") fix the problem? ...
written 3 days ago by James W. MacDonald43k
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Comment: C: paCalls with Clariom Chips
... As a followup, you should just get an error saying that paCalls doesn't work with this particular array. The ExpressionFeatureSet was originally intended for the old style 3'-biased arrays, which mostly did have MM probes (although even back then Affy was phasing them out). When I added the Clariom ...
written 3 days ago by James W. MacDonald43k
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Answer: A: paCalls with Clariom Chips
... You can't do a MAS5 style P/A call with an array that has no MM probes. ...
written 3 days ago by James W. MacDonald43k
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Comment: C: Error during makeOrgPackageFromNCBI
... I have updated both the release and devel versions of AnnotationForge, and you should be able to get the updated package using biocLite in a day or two. ...
written 5 days ago by James W. MacDonald43k
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Comment: C: Error during makeOrgPackageFromNCBI
... OK, NCBI has added an extra column to the gene_info file that we need to do something with. The quick fix is to do this at a terminal prompt zcat gene_info.gz | cut -f 1-15 > gene_info rm gene_info.gz gzip gene_info and then re-run makeOrgPackageFromNCBI. If it downloads the gene_info.gz file ...
written 5 days ago by James W. MacDonald43k
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Comment: C: reduce function in GenomicRanges
... Do you have an example? ...
written 5 days ago by James W. MacDonald43k
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Comment: C: Simple UCSC to transcript annotation
... If you want to add a comment, please use the ADD COMMENT link. The Add your answer box below is for people to add answers, not more questions or comments. I have no idea what you mean by 'nested in at least 3 levels'. Are you complaining that it took three lines of code to generate an answer? If s ...
written 5 days ago by James W. MacDonald43k
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Comment: C: Unsupervised clustering heatmap of gene expression data
... The purpose of this support site is to provide support for those who have functional questions about how to do a particular task using Bioconductor tools. It is not intended as a place for people to get advice on how they should analyze their data, although there are probably examples where people ( ...
written 5 days ago by James W. MacDonald43k

Latest awards to James W. MacDonald

Scholar 6 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 6 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 6 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 10 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 3 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 3 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 3 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 3 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 4 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 4 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 4 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 4 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 5 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 5 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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