Moderator: James W. MacDonald

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43,950
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Location:
United States
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Last seen:
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Joined:
15 years, 3 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 • 4,971 results • page 1 of 498 • next >
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Answer: A: Error downloading the package
... Yes. there is no package called ‘GenomicAlignments’ means that there is no package called GenomicAlignments installed in your version of R, so you need to install GenomicAlignments. ...
written 1 day ago by James W. MacDonald44k
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Comment: C: Expression profile from $E from Voom
... But I should point out that the object  you call "v" is an EList that has the weights, and the thing you call Elist is a regular matrix that just contains the E list item from v. You should not strip things out of objects like that unless you know what you are doing. The EList object (called v) is ...
written 1 day ago by James W. MacDonald44k
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Answer: A: Expression profile from $E from Voom
... You could just read the help page for voom to find this out. From ?voom Details: This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma. voom is an acronym for mean-variance modelling at the observational level. The key concern is t ...
written 1 day ago by James W. MacDonald44k
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Comment: C: How to add both row and column labels to Complexheatmap
... I am not sure you checked all the documentation and examples for ComplexHeatmap because literally the very first example has both row and column names! From ?Heatmap: mat = matrix(rnorm(80, 2), 8, 10) mat = rbind(mat, matrix(rnorm(40, -2), 4, 10)) rownames(mat) = letters[1:12] ...
written 1 day ago by James W. MacDonald44k
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Answer: A: How to add both row and column labels to Complexheatmap
... This is a basic R question, and would be better posed on say R-help (r-help@r-project.org), or better yet, by simply reading the help page for read.table. From ?read.table row.names: a vector of row names. This can be a vector giving the actual row names, or a single number giving the c ...
written 2 days ago by James W. MacDonald44k
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Answer: A: running matlab code from RStudio
... This support site is intended for Bioconductor package support, not basic R support. You could ask on R-help (r-help@r-project.org), or perhaps you could find a matlab support site that could help. ...
written 3 days ago by James W. MacDonald44k
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Comment: C: Effect of inclusion of patientID in the formula
... So you have cases and controls, and each patient had two visits, right? In that situation you usually want to know about the interaction (e.g., you want to know if the differences between visit 1 and visit 2 are the same for cases and controls or not). If this is correct, then there is quite a bit o ...
written 4 days ago by James W. MacDonald44k
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Answer: A: AnnotationHub downloading dataset fail
... Actually, now that I look at your package versions, you need to do library(BiocInstaller) biocValid() and then do what it tells you to do, which will probably be biocLite(ask = FALSE) ...
written 4 days ago by James W. MacDonald44k
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Answer: A: AnnotationHub downloading dataset fail
... Maybe try again? > hub[["AH27075"]] require("rtracklayer") downloading from 'https://annotationhub.bioconductor.org/fetch/32503' retrieving 1 resource |======================================================================| 100% Attaching package: 'Biostrings' The following object is masked ...
written 4 days ago by James W. MacDonald44k
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Answer: A: paired design with continious covariate
... This is covered in the vignette here. ...
written 4 days ago by James W. MacDonald44k

Latest awards to James W. MacDonald

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