Moderator: James W. MacDonald

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42,170
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Location:
United States
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Last seen:
8 hours ago
Joined:
14 years, 10 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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Answer: A: DESeq2: how to interpret the
... Why would scaling to 0-1 make it more interpretable? You would have the exact same colors, but the scale would just have different numbers. The idea for this part of the workflow is to say which samples are similar to each other, and you can see in your heatmap that there are three blocks of sample ...
written 1 day ago by James W. MacDonald42k
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Answer: A: How to interpret the SVA results
... You don't really interpret singular values. You could do a PCA plot of your data, then fit a linear model using just the singular values and then plot a PCA plot of the residuals to see if the singular values corrected for whatever batch effect you may have, but in your case it looks like that is ho ...
written 1 day ago by James W. MacDonald42k
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Answer: A: Message asking to update and download from source functions when downloading pac
... It's pretty straightforward, and your question is answered in the question that R asks you: There is a binary version available but the source version is later: binary source needs_compilation lattice 0.20-34 0.20-35 TRUE Do you want to install from sources the package wh ...
written 1 day ago by James W. MacDonald42k
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Answer: A: Controlling for confounding variables in bumphunter
... The bumphunter package just uses the model fitting code that exists in base R, so your question could be reformulated to How do I specify a design matrix in R that includes my coefficient of interest, plus other confounders? And the answer is to use model.matrix, and to note that in any model ther ...
written 2 days ago by James W. MacDonald42k
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Answer: A: Using hugene10sttranscriptcluster.db for annotation
... While you can use as.list to get the values, it's really not the way to go. You end up relying on old code that doesn't really do what you might think it does. Plus, why would you want a list in the first place? As an example: > z <- as.list(hugene10sttranscriptclusterSYMBOL[keys(hugene10st ...
written 2 days ago by James W. MacDonald42k
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Answer: A: Error when using the showGroupDensity function in topGO
... This error is coming from factor, and it is basically saying that this thing called 'group' has no length, and the 'labels' argument has length 2. You can easily replicate this error: > group <- character(0) > factor(group, labels = c("a","b")) Error in factor(group, labels = c("a", "b")) ...
written 5 days ago by James W. MacDonald42k
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Comment: C: Question: minfi MethylationEPIC errors
... It would also be helpful if you would show the code you used up to that point. ...
written 5 days ago by James W. MacDonald42k
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Comment: C: Nugen adapter in RNA seq
... This isn't a STAR forum either. I presume STAR has a manual that you could peruse. ...
written 6 days ago by James W. MacDonald42k
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Answer: A: Nugen adapter in RNA seq
... This isn't the right forum for these questions. You should contact NuGen if you want information about their product, and you should look at the help for Trimmomatic if you want to learn how to use their tool. Or you could note that modern aligners are quite capable of soft-clipping the ends of rea ...
written 6 days ago by James W. MacDonald42k
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Answer: A: QIIME, R and bioconducter
... This isn't really the place to be asking for help. QIIME isn't a Bioconductor package, and you are using R code that comes as part of QIIME, not Bioconductor. It's just happenstance that the code uses a Bioc package to do its thing. It's also not clear that this has anything to do with your install ...
written 6 days ago by James W. MacDonald42k

Latest awards to James W. MacDonald

Scholar 8 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 8 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 14 days ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 14 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 5 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 5 weeks 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
Cylon 5 weeks ago, received 1,000 up votes.
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 6 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Scholar 7 weeks ago, created an answer that has been accepted. For A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
Scholar 8 weeks ago, created an answer that has been accepted. For A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Converting Protein Accessions Into Protein Symbols
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: featureCount - very less Successfully assigned reads
Teacher 11 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 11 months ago, created an answer with at least 3 up-votes. For A: Concatenation of Bimap
Teacher 11 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
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 11 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 11 months ago, created an answer that has been accepted. For A: Converting Protein Accessions Into Protein Symbols
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Interpretation of voom limma's intercept coefficient

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