Moderator: James W. MacDonald

Reputation:
44,650
Status:
Trusted
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
15 years, 5 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 • 5,051 results • page 1 of 506 • next >
0
votes
1
answers
39
views
1
answers
Answer: A: Trying to annotate microarray data and some probe set presents mismatch
... The way you originally annotated returns nothing for any one to many mappings. Which is one thing you can do ( e.g., it's not clear what the probeset measures, so return nothing). Another alternative is to select one of the choices, at random, or maybe just the first. The remaining alternative is to ...
written 9 hours ago by James W. MacDonald45k
0
votes
2
answers
68
views
2
answers
Comment: C: How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
... That's not a hint. It's a message that some of the probesets map to more than one thing. By default you get just the first thing, although there are arguments that you can use to get all the mappings. But you claim it doesn't work without apparently even looking at the output. You should probably ma ...
written 1 day ago by James W. MacDonald45k
0
votes
1
answers
99
views
1
answers
Comment: C: How to set 'strandMode' with summarizeOverlaps()
... I sent a patch to Val. After adding a couple of ellipsis args, I get > SE.all <- summarizeOverlaps(ex, bfl, singleEnd = FALSE, fragments = FALSE, strandMode = 2) > z <- bplapply(bfl, readGAlignmentPairs, strandMode=2) > zz <- bplapply(z, function(x) summarizeOverlaps(ex, x, sin ...
written 6 days ago by James W. MacDonald45k
0
votes
1
answers
92
views
1
answers
Answer: A: Anova test on gene expression data
... Sure. You could just use lm from the base package. ...
written 7 days ago by James W. MacDonald45k
0
votes
1
answers
99
views
1
answers
Comment: C: How to set 'strandMode' with summarizeOverlaps()
... Ah, you're right. In .countWithYieldSize, the specified function is called using x <- FUN(bf, param = param) with no ellipsis argument, so strandMode is ignored. But do note that all .countWithYieldSize is doing (that you will have to do yourself) is calling bplapply, using the chosen function ...
written 7 days ago by James W. MacDonald45k
0
votes
1
answers
99
views
1
answers
Comment: C: How to set 'strandMode' with summarizeOverlaps()
... I think I set you wrong. You want both pairedEnd AND fragments to be FALSE, otherwise you get readGAlignmentsList, which doesn't have a strandMode argument. I still wouldn't expect an error, however, as that argument is being passed down via the ellipsis argument, and my understanding is that a func ...
written 8 days ago by James W. MacDonald45k
0
votes
1
answers
99
views
1
answers
Answer: A: How to set 'strandMode' with summarizeOverlaps()
... It's sort of buried, since what you are doing is relying on the method summarizeOverlaps,GRanges,BamFileList, which decides how to read in the bam files based on the singleEnd and fragments arguments. If they are FALSE and TRUE, respectively, then the data will be read in using readGAlignmentPairs, ...
written 8 days ago by James W. MacDonald45k
0
votes
1
answers
62
views
1
answers
Answer: A: I want to know how i solved this error?
... This question has nothing to do with Bioconductor packages. You should be asking this on R-help (r-help@r-project.org). But do note that you will need to provide much more information than what you give here. Unless somebody can reproduce your error, it's usually not possible to diagnose.   ...
written 8 days ago by James W. MacDonald45k
0
votes
1
answers
58
views
1
answers
Answer: A: claariom.s.human annotation error
... You have a mixture of packages, some that are current, and some that are up to two releases out of date (affycoretools and oligo to name two). You are liable to get odd errors running a non-standard installation like that, and we don't support people who choose to do so (on the assumption that if yo ...
written 9 days ago by James W. MacDonald45k
0
votes
1
answers
113
views
1
answers
Comment: C: How to prevent readDNAStringSet() function from switching masked sequences (lowe
... The first place you should be looking is the help page for the function you are trying to use! I already tried to nudge you in that direction, so let me be more direct. Reading the help page first will save you lots of time, and that is what you should always do. If it seems to people who might help ...
written 12 days ago by James W. MacDonald45k

Latest awards to James W. MacDonald

Scholar 5 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 5 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 5 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Why the log fold change of some genes returned by edgeR is not compatible with t
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Why the log fold change of some genes returned by edgeR is not compatible with t
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 6 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 7 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 7 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 7 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 7 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 8 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 8 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 8 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 8 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 9 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 9 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 176 users visited in the last hour