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Moderator: James W. MacDonald

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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 1 of 570 • next >
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Answer: A: Iterate through sever annotation database packages
... Ideally you wouldn't start with a factor, so when you create your `data.frame` (however you are doing that), you would want to use `stringsAsFactors = FALSE`. Also note that `select` expects you to pass an OrgDb, not a character value that has the same name as an OrgDb, so you need to `get` the OrgD ...
written 6 hours ago by James W. MacDonald49k
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Answer: A: Normalization large data set
... That's a lot of arrays. You could try using `optimize.by = "memory"`, which is a bit more memory efficient. But it looks like you are working on a Windows box, which probably doesn't have much memory (like, maybe 16 Gb, which is a 'normal' amount of RAM for a desktop), in which case it probably won' ...
written 11 hours ago by James W. MacDonald49k
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Answer: A: Microarray Analysis of Sleep Deprivation Data Experimental Design
... You have a relatively complex experiment, and you could ask questions more sophisticated than 'what genes are affected by sleep deprivation'. For example, you could say that the people who failed the neuro tests might be different in some way from those who passed, and you could then look for genes ...
written 11 hours ago by James W. MacDonald49k
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Answer: A: DESeq2 overestimates log2Fold Change
... The coefficients that are estimated by DESeq2 come from a GLM, which uses an interative procedure to estimate the coefficients because there is no closed-form solution. In addition, the GLM uses estimates from the library size as offsets, which you are probably not accounting for. Put a different wa ...
written 4 days ago by James W. MacDonald49k
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Answer: A: differentail expression analysis with interaction terms
... With that many different combinations the number of interactions gets so large that trying to get a high level assessment of what is going on becomes (IMO) almost impossible. You would probably be better off using a spline fit and testing for the interaction that way. If there are lots of genes, you ...
written 4 days ago by James W. MacDonald49k
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Answer: A: Conduct likelihood ratio tests for a variable that isn't explicitly defined by m
... It's much easier if you just compute the means for each group and then do the comparisons directly. For whatever reason the example you link to (and you) both do that sort of thing, but then inexplicably don't use it. ``` > group <- paste(rep(c("basal","luminal"), each = 6), rep(c("virgin","pr ...
written 6 days ago by James W. MacDonald49k
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Comment: C: Change sign from Granges scores to visualize negative strand data
... Or maybe you mean something in the mcols slot? ``` > mcols(z)$scores <- runif(10) > z GRanges object with 10 ranges and 1 metadata column: seqnames ranges strand | scores | [1] chr1 1-31 - | 0.781348916934803 [2] chr1 ...
written 6 days ago by James W. MacDonald49k
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Answer: A: Change sign from Granges scores to visualize negative strand data
... ``` > z <- GRanges(rep("chr1", 10), IRanges(1:10, 31:40)) > z GRanges object with 10 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 1-31 * [2] chr1 2-32 * [3] chr1 3-33 * [4] chr1 4-34 ...
written 6 days ago by James W. MacDonald49k
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Comment: C: stringasfactor = F changes the output of pheatmap, why?
... It's not whether or not the code is clear. That's not what I meant by self-contained code. By that I mean some code that anybody could run that shows the problems you are having. You are showing some code that you purport will cause changes in the behavior of `pheatmap`, but nobody else can run your ...
written 7 days ago by James W. MacDonald49k
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Answer: A: Normalized counts from DESeq2 results in similar but not equal total read count?
... The only time you would expect the normalized counts to sum to the same exact value across libraries would be if you expect that there are no differentially expressed genes, in which case any differences in library size are due only to technical differences (starting amount of mRNA, variability in l ...
written 7 days ago by James W. MacDonald49k

Latest awards to James W. MacDonald

Scholar 5 weeks ago, created an answer that has been accepted. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 5 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 5 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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