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Moderator: James W. MacDonald

Reputation:
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Location:
United States
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Google Scholar Page
Last seen:
1 day, 2 hours ago
Joined:
16 years, 8 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 • 5,692 results • page 2 of 570 • next >
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Answer: A: stringasfactor = F changes the output of pheatmap, why?
... You would have to provide some self-contained code to show what you say is happening. To me it looks like in the first heatmap you used **Edit** `cluster_cols = TRUE` and in the second heatmap you used **Edit** `cluster_cols = FALSE`. Whether or not you use `stringsAsFactors = TRUE` or `FALSE` shoul ...
written 11 days ago by James W. MacDonald49k
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Comment: C: Memory issues in summarizeOverlaps funtion
... I think you might be confused. The row names for a `SummarizedExperiment` are the underlying IDs (which in your case might be Entrez Gene IDs? The yieldSize argument simply sets the chunk size for the data being read in, not the total amount of data to read in: ``` > bams <- c("303301Aligned.s ...
written 11 days ago by James W. MacDonald49k
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Comment: C: AnnotationDbi: Select - Join order
... Well, you already showed one fix, which is to require that the central ID be part of any query. I showed an alternative, which is to make individual queries using `mapIds` and converting to a `data.frame`. Is there something wrong with either of those ideas? ...
written 11 days ago by James W. MacDonald49k
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Comment: C: Memory issues in summarizeOverlaps funtion
... Why are you doing that? Simply passing a `BamFileList` to `summarizeOverlaps` where you have specified the yieldSize for the `BamFileList` will cause the data to be read in chunks. ...
written 12 days ago by James W. MacDonald49k
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Comment: C: MIssing ensemble orthologues in biomart
... I don't know - that is a question that you will have to answer yourself. I don't know why EBI doesn't think those are orthologs, so without knowing that, how could I say that they 'do not find orthologue gene ids'? Maybe they do find them all, and there is a reason to think that those 1400 genes hav ...
written 12 days ago by James W. MacDonald49k
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Answer: A: MIssing ensemble orthologues in biomart
... When you go to either of the pages you link, while they do show the same gene symbol, they do not have a link for any orthologs under the comparative genomics section, indicating that EBI/EMBL do not think these two genes are orthologs. As a counter example, consider [Sox17][1], which lists 24 pri ...
written 12 days ago by James W. MacDonald49k
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Comment: C: How to read variants into R from large dataset using VariantAnnotation
... You don't say how much RAM you have, or your operating system. If you are constrained (by having not much RAM or being on Windows), then you probably need to add RAM or get a better computer. In addition you need to include the output from `sessionInfo` ...
written 12 days ago by James W. MacDonald49k
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Comment: C: AnnotationDbi: Select - Join order
... In future, if you want to add a reply, please use the ADD REPLY or ADD COMMENT buttons rather than adding an answer, which you by definition are not doing. ...
written 12 days ago by James W. MacDonald49k
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Answer: A: Extract gene ID
... The annaffy package was developed years ago, and uses an outmoded way of extracting data. You are better off using either `select` or `mapIds`, but do note that the reason you get so many NA values is because in the past any probeset that mapped to more than one gene ID would return NA (where the th ...
written 12 days ago by James W. MacDonald49k
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Answer: A: how to install package of "rnaseqGene" for R (ver: 3.5.2) for windows
... Why are you doing all these random things? You evidently know about `BiocManager::install`, which is the only way you should be installing any Bioconductor package. ``` > library(BiocManager) Bioconductor version 3.8 (BiocManager 1.30.4), ?BiocManager::install for help Warning message: package ...
written 15 days ago by James W. MacDonald49k

Latest awards to James W. MacDonald

Scholar 6 weeks ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 6 weeks 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 weeks ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 6 weeks 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 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 11 weeks ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 11 weeks 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 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Scholar 3 months ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 3 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Probe to gene id conversion
Scholar 3 months ago, created an answer that has been accepted. For A: BiomaRt returns 0 obs
Popular Question 3 months ago, created a question with more than 1,000 views. For Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Teacher 3 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 4 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Scholar 4 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
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
Scholar 4 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
Scholar 5 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?

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