Moderator: James W. MacDonald

Reputation:
45,150
Status:
Trusted
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
2 days, 2 hours ago
Joined:
15 years, 9 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 • 5,142 results • page 2 of 515 • next >
0
votes
2
answers
621
views
2
answers
Comment: C: Limma voom or trend?
... First, unless you are answering a question, don't use the 'Add your answer' box. Because you aren't answering a question. Use the ADD REPLY link to add replies or additional questions. I would disagree with your statement regarding clarity of the 'manual', although I am not sure what you mean by th ...
written 9 days ago by James W. MacDonald45k
0
votes
0
answers
111
views
0
answers
Comment: C: Problem converting annotation to GenomicRanges object
... No. The Rd files are the help pages, and wouldn't have anything to do with code functionality. I doubt this has anything to do with GenomicRanges. The error you see comes from makeGRangesFromDataFrame, which expects there to be a 'start' and 'end' column in the data.frame. If the parser in metaseqr ...
written 11 days ago by James W. MacDonald45k
0
votes
1
answers
109
views
1
answers
Answer: A: Fold Change and LogFC
... To answer your question requires a tautology. The difference between fold change and log fold change is in the latter case the fold change has been logged. It's not important per se; it arises because most high throughput data tends to be highly right skewed, and taking logs helps with that. ...
written 11 days ago by James W. MacDonald45k
0
votes
1
answers
58
views
1
answers
Answer: A: Support site search not finding posts?
... The support site search is...not good. I usually do a Google search like drnevich tximport limma-trend site:support.bioconductor.org Which brings up lots of posts that may include what you want. ...
written 12 days ago by James W. MacDonald45k
0
votes
1
answers
51
views
1
answers
Answer: A: DESeqDataSetFromHTSeq -- function not found
... This usually means that you haven't loaded the package that contains the function. But using the Bioconductor code search, and looking at the pdf help for both DESeq and DESeq2 indicates that this function doesn't actually exist in any Bioconductor package. Also please note that it would have been ...
written 12 days ago by James W. MacDonald45k
0
votes
2
answers
120
views
2
answers
Answer: A: processing agilent data by limma
... Providing stylized code that isn't really what you ran is not helpful. Unless you really have a path on your computer called /path/to/file, which would be sort of cool. As for question #1, you get an error reading in a file. Did you try reading in just that one file? How about all files but that on ...
written 13 days ago by James W. MacDonald45k
0
votes
3
answers
178
views
3
answers
Answer: A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
... It looks like there are three GO IDs in the org.Sc.sgd.db package that have been deprecated by the GO consortium, and you have found one of them. It's not clear how those terms got included, as for example the term you are talking about was deprecated over a year ago. > z <- unique(keys(org. ...
written 16 days ago by James W. MacDonald45k
0
votes
1
answers
73
views
1
answers
Answer: A: TopGO - Incorrect mapping genes to GO terms
... You are looking at the genes that have a direct mapping to that GO term, whereas topGO uses all genes that map directly to that term as well as all of its progeny.  Put another way, topGO uses GOALL, whereas you are using GO: > nrow(select(org.Mm.eg.db, "GO:1903561", "ENTREZID", "GOALL")) 'sel ...
written 18 days ago by James W. MacDonald45k
0
votes
1
answers
81
views
1
answers
Answer: A: GViz, different group colours
... Use the col argument. See p. 30 of the Gviz user's guide for a list of all useful arguments. ...
written 20 days ago by James W. MacDonald45k
0
votes
0
answers
111
views
0
answers
Comment: C: Problem converting annotation to GenomicRanges object
... Is there a reason that you are trying to build a TxDb package rather than using the already built TxDb.Hsapiens.UCSC.hg19.knownGene package? ...
written 20 days ago by James W. MacDonald45k

Latest awards to James W. MacDonald

Scholar 8 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 8 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 8 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Commentator 8 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 9 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 9 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 9 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 10 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 10 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 10 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 10 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 11 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 11 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 11 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 11 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 12 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 12 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: 146 users visited in the last hour