Moderator: James W. MacDonald

Reputation:
49,990
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Location:
United States
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Google Scholar Page
Last seen:
17 hours ago
Joined:
17 years 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 • 5,860 results • page 1 of 586 • next >
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... **Keymaker, my friend** ![enter image description here][1] [1]: https://vignette.wikia.nocookie.net/matrix/images/d/dd/Keymaker.jpg/revision/latest?cb=20090501223458 ...
written 4 days ago by James W. MacDonald50k
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... Yes, but if it's *your* imgur post, and you click on it, you are presented with a dialog box that looks like this: ![enter image description here][1] And if you look to the right, there's a Direct Link that you can copy to post. Hence the part in the FAQ about a 'Direct Link'. [1]: https://i.im ...
written 4 days ago by James W. MacDonald50k
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... I can get a direct link to one of my own imgur posts, and it looks like this ![enter image description here][1] [1]: https://i.imgur.com/M9ZPeQ3.png ...
written 4 days ago by James W. MacDonald50k
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... **Edit** I can't get the 'direct link' from your post, so it doesn't work for me. ...
written 4 days ago by James W. MacDonald50k
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Comment: C: RNA-Seq and edgeR: remarkable differences between cpms and fitted values
... From the [FAQ][1] > How do I put images into my posts? > > You can also put images and plots into your posts. All you need to do > is create (or login to) a free account with http://imgur.com and > upload any images or plots that you want to share. Then you can enter > the imgur ...
written 4 days ago by James W. MacDonald50k
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Comment: C: Need a BSgenome.Btaurus.UCSC.bostau9 package
... Try downloading it directly, using a browser. ...
written 4 days ago by James W. MacDonald50k
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Answer: A: Need a BSgenome.Btaurus.UCSC.bostau9 package
... I'm not sure you need to make a `BSgenome` package these days, but instead can simply download and import the 2bit file. ``` > library(rtracklayer) > download.file("ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips/bosTau9.2bit", "bosTau9.2bit") trying URL 'ftp://hgdownload.soe.ucsc.ed ...
written 5 days ago by James W. MacDonald50k
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Answer: A: topGO package unable to find library(ALL) and data(ALL)
... topGO doesn't depend on ALL, it suggests it. So if you want that package you need to install separately. ...
written 11 days ago by James W. MacDonald50k
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Comment: C: Limma model design: is it better to just build a separate design for each specif
... When you use `voom` you are using the variance of the data twice - first when you compute the observation-level weights, and then as part of your statistic. In that situation there may be more reason to keep all samples in your model, in order to get the best weight estimates possible. It is often ...
written 13 days ago by James W. MacDonald50k
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Answer: A: Limma model design: is it better to just build a separate design for each specif
... The answer is 'it depends'. In general, if the within-group variability for the 'c' samples is comparable to the 'a' and 'b' samples, then you gain by keeping those samples in your model. That's because the variance estimate used for the contrast is based on (sort of) the average within-group variab ...
written 13 days ago by James W. MacDonald50k

Latest awards to James W. MacDonald

Scholar 5 months ago, created an answer that has been accepted. For A: Retrieving all genes related a go term
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to export enrichGO results for future visualization with barplot, dotplot, e
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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Scholar 5 months ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Scholar 5 months ago, created an answer that has been accepted. For A: IRanges which are not S4 generic: endoapply mendoapply error in loading oligocla
Scholar 5 months ago, created an answer that has been accepted. For A: Correct usage of tximport counts in edgeR without offset matrix.
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Best way to convert uniprot accessions to entrez gene identifiers in R
Scholar 5 months ago, created an answer that has been accepted. For A: Iterate through sever annotation database packages
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Effect of lfcThreshold on p-value in DESeq2
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: Limma import .gpr file error
Scholar 5 months ago, created an answer that has been accepted. For A: Probe to gene id conversion
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Probe to gene id conversion
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Scholar 5 months ago, created an answer that has been accepted. For A: How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: EdgeR blocking and "All combinations of multiple factors"
Scholar 5 months ago, created an answer that has been accepted. For A: limma - blocking or regressing out nuisance variable
Scholar 5 months ago, created an answer that has been accepted. For A: Problems with "exonsBy" function from GenomicFeatures package
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Different annotation obtained from hgu133a2.db and affymetrix annotation release
Scholar 5 months ago, created an answer that has been accepted. For A: Bioconductor: quantile normalization
Scholar 5 months ago, created an answer that has been accepted. For A: Human Exon: arome.affymetrix residuals Inf value

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