Moderator: James W. MacDonald

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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

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Answer: A: Effect of inclusion of patientID in the formula
... One way to think about this is in the context of a paired t-test. In a 'regular' t-test you compute the mean of each group and then compare the means to see if you think there is an underlying population difference between the two groups. But if the two groups are somehow related (say you measured p ...
written 4 days ago by James W. MacDonald44k
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Answer: A: Retrieving all genes related a go term
... The GO.db package is built twice a year, so at best the one you have is from April. The data at the Biomart server is updated, um, more often? I presume there is some information somewhere that would tell you, or perhaps Mike Smith knows. I sort of assumed that they updated more regularly, but now t ...
written 8 days ago by James W. MacDonald44k
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Answer: A: Error in columns(org.Hs.eg.db) : could not find function "columns"
... There are two problems here. First, don't do this: install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.1/data/annotation") The whole idea behind biocLite is that you don't need to figure out what repository to use, particularly since Bioconductor package versions are specif ...
written 10 days ago by James W. MacDonald44k
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Answer: A: Exporting a FASTA file from a getBM vs getSequence query
... library(Biostrings) z <- DNAStringSet(fasta[,1]) names(z) <- apply(fasta[,-1], 2, paste, collapse = "; ") writeXStringSet(z, "biomartExportTest.seq") ...
written 10 days ago by James W. MacDonald44k
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Comment: C: Use of RMA to get exon-level summaries for HTA 2.0
... Any comparisons between the same samples using different methods by definition is only a comparison of the methods. A simplistic example would be to measure your weight using a bathroom scale, and then measuring your weight using one of those scales they have at the doctor's office. Any difference i ...
written 12 days ago by James W. MacDonald44k
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Answer: A: Use of RMA to get exon-level summaries for HTA 2.0
... Sort of. If you summarize at the 'probeset' level using the oligo package, then you will get probe set region (PSR) and junction probeset (JUC) summaries. These are not exon level, in general, as you can have one or more PSRs per exon, and the JUC probes measure exon-exon boundaries, which by defini ...
written 12 days ago by James W. MacDonald44k
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Comment: C: Is DESeq2 PCAplot already scaled?
... I utilized my l33t Google skillz: pca plot scale love site:support.bioconductor.org the search on this site is worthless, so I always just use Google directly with the site qualifier. It's the first hit on the second page (at least based on what Google thinks I want). ...
written 15 days ago by James W. MacDonald44k
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Comment: C: Is DESeq2 PCAplot already scaled?
... Is this it? ...
written 16 days ago by James W. MacDonald44k
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Comment: C: clusterProfiler: Which GO version is used behind ?
... You can always install whatever version of package you want - that's the beauty of R and Open Source software in general. However, do note that we don't support anything but the release version of R/BioC, which means if you are running some non-standard configuration and you have problems, it's on ...
written 16 days ago by James W. MacDonald44k
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Comment: C: affycoretools annotateEset problem using Clariom D arrays
... You mean other than the help page? Here is the first section: annotateEset package:affycoretools R Documentation Method to annotate ExpressionSets automatically Description: This function fills the featureData slot of the ExpressionSet automatically, which is then ...
written 16 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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