Moderator: James W. MacDonald

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Last seen:
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Joined:
16 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

<prev • 5,768 results • page 2 of 577 • next >
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Answer: A: How to normalize RNA-seq when 50% genes are DE? (TMM)
... This has been answered here more than once. An example being [this][1]. [1]: https://support.bioconductor.org/p/116317/ ...
written 11 days ago by James W. MacDonald49k
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Answer: A: The query to the BioMart webservice returned an invalid result: biomaRt expected
... Mike Smith will probably be along in a bit with a direct answer, but I wonder if you are sort of duplicating work that has already been done by Johannes Rainier, when he builds the EnsDb packages: ``` > library(AnnotationHub) > hub <- AnnotationHub() > query(hub, c("mus musculus","ensd ...
written 12 days ago by James W. MacDonald49k
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Answer: A: How to tell a GAlignmentsList singleton is mate1 or mate2
... Maybe like this? ``` > param <- ScanBamParam(what = "flag", which = GRanges("chr1:1-1e7")) > bf <- BamFile("aligned_nodups/A1-4Aligned.sortedByCoord.out.bam", asMates = TRUE) > param <- ScanBamParam(what = "flag", which = GRanges("chr1:1-1e7")) > z <- readGAlignmentsList(bf ...
written 12 days ago by James W. MacDonald49k
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Answer: A: Variance for paired design
... Given that you have only 7 subjects, by definition your results aren't robust, where by robust I mean 'are representative of the underlying population rather than idiosyncratic results that are likely only to apply to the 7 subjects under study'. In other words, if you designed a study to see if a d ...
written 12 days ago by James W. MacDonald49k
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Answer: A: Problem concerning the Probe_Id / ProbeID and illuminaHumanv4PROBEQUALITY
... Your question is difficult to answer because you seem to be omitting critical information, like what you have done, what you got, what you are trying to do, etc. That said, do note that R is case sensitive, and 'Probe_Id' is not the same thing as 'PROBE_ID'. And if I am not mistaken, the column yo ...
written 12 days ago by James W. MacDonald49k
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Answer: A: makeTxDbFromGFF, GTF columns not included in the TxDb object
... The annotation packages are roughly split into packages that have to do with genomic locations (the TxDb packages), and packages that have to do with annotations (e.g., names for genes, what they do, pathways they are in, etc, which go into OrgDb packages). The gene symbol is part of the latter, so ...
written 12 days ago by James W. MacDonald49k
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Answer: A: GenomicRanges error constructing Granges
... You are doing a bunch of stuff on the front end, and also for some reason deciding halfway through to try to detach everything (?). Can you not just start R, load `GenomicRanges` and make a `GRanges` object? If that works, then you can try adding in the other stuff you are doing. Also, the output f ...
written 13 days ago by James W. MacDonald49k
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Comment: C: Error in ncol(eset) 'eset.filt' not found
... You don't [install Bioconductor packages][1] using `install.packages`. And my response remains the same. If R gives you that error, it's because the object you are calling 'eset.filter' doesn't exist. Telling us snippets of what you have done isn't helpful - you need to figure out for yourself why ...
written 16 days ago by James W. MacDonald49k
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Answer: A: add gene names to rlog transformation for heatmap using the library "org.Hs.eg.d
... There is a vignette for [AnnotationDb][1]i that gives some examples, as well as the workshop that [Lori and I give][2] at the Bioconductor conferences. You could read that, and come back with specific questions. [1]: http://bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc ...
written 16 days ago by James W. MacDonald49k
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Answer: A: Normalizing expression across complex array designs
... That's not really how meta-analysis works. To magically normalize out all the technical differences between the four data sets yet keep all the real biological differences would be some arcane magic indeed. Instead what one usually does is to make comparisons within each data set, and then combine t ...
written 16 days ago by James W. MacDonald49k

Latest awards to James W. MacDonald

Scholar 3 months ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Scholar 3 months ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. 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: goseq: Formatting category list for use with goseq
Appreciated 4 months ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. 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: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 4 months ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Scholar 5 months ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 5 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Probe to gene id conversion
Scholar 5 months ago, created an answer that has been accepted. For A: BiomaRt returns 0 obs
Popular Question 5 months ago, created a question with more than 1,000 views. For Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
Scholar 6 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Scholar 6 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Scholar 6 months ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 7 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Scholar 7 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?

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