Moderator: James W. MacDonald

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42,900
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Location:
United States
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Google Scholar Page
Last seen:
6 days, 15 hours ago
Joined:
14 years, 11 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 • 4,791 results • page 1 of 480 • next >
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Comment: C: TCGA controlled data
... If you have a followup question, use the ADD REPLY button and type in the box that comes up. The box below that says 'Add your answer' is for answers, not questions. You don't have a specific question that can be easily answered, nor do you have any code that you tried that didn't work. If you want ...
written 6 days ago by James W. MacDonald43k
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Comment: C: TCGA controlled data
... If you are intending to get data from the Affy SNP 6.0 array, you should note that this is genotype data, not expression data. So if you want to do differential expression you need a different array platform. ...
written 7 days ago by James W. MacDonald43k
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Comment: C: Alternative packages to limma for analysis of microarray datasets
... Other possibilities include multtest and rankprod. ...
written 7 days ago by James W. MacDonald43k
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Comment: C: Meaning of the value column in bumphunter output (minfi package)
... The way you specified your model matrix will by default set the second coefficient to be tumor - control. You can test that by looking at your factor levels (the first factor level is by default the baseline level) or by looking at the design matrix itself.   ...
written 8 days ago by James W. MacDonald43k
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Comment: C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
... Why do you think that FDR or a p-value is a measure of reproducibility? You seem to be laboring under the unfounded assumption that a small p-value means an experiment will be able to be reproduced, which isn't remotely correct. You also seem to think that DESeq2 is 'estimating FDR', which again is ...
written 8 days ago by James W. MacDonald43k
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Comment: C: fonction queryMany not found
... If you have further questions, please use the ADD COMMENT button, rather than adding another answer (when you are not in fact adding an answer at all!). The error you get is from an internal function that is simply intended to change a name in the returned DataFrame. If you were to debug the functi ...
written 8 days ago by James W. MacDonald43k
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Answer: A: NGS with summarizeOverlaps and SAM files
... Your problem arises because you are aligning reads to a genome that has chromosomes that are too long for the BAM format. But that's only one way to do things. You could alternatively use either salmon or kallisto to do the (much faster) alignment against the wheat transcriptome, and then use tximpo ...
written 9 days ago by James W. MacDonald43k
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Answer: A: difference in detection p-values from Minfi vs. GenomeStudio
... The obvious answer is that they use different algorithms to determine which probes are actually measuring something, and apparently BeadStudio is a bit more conservative. However it is probably not possible to say much more than that because BeadStudio's code isn't (AFAIK) available for you to perus ...
written 9 days ago by James W. MacDonald43k
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Answer: A: fonction queryMany not found
... Any time you see the error Impossible de trouver la fonction 'queryMany' it means that you haven't loaded the package that contains that function yet. So if you have installed mygene, you still need to do library(mygene) in order to use any of the functions in that package. ...
written 9 days ago by James W. MacDonald43k
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Comment: C: Is mapId supposed to concatenate multiVals?
... I usually try to stick with whatever group's ID I have in hand, rather than trying to cross-match, because these conflicts are inevitable. So if I have Ensembl IDs, I use the EnsDb packages or biomaRt for annotation. If I have Entrez Gene IDs, then I use the TxDb and org packages for annotation. Th ...
written 10 days ago by James W. MacDonald43k

Latest awards to James W. MacDonald

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 10 days ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 4 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 4 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 5 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 7 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 9 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 9 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 10 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 10 weeks 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: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 3 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Cylon 3 months ago, received 1,000 up votes.
Teacher 3 months 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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method

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