Moderator: James W. MacDonald

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14 years, 9 months ago
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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 • 4,680 results • page 2 of 468 • next >
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Answer: A: Homo.sapiens annotation package for HLA genes
... The genes function basically takes the furthest extent of all transcripts for a particular gene, and returns that. This works really well for the vast majority of all genes, but fails in two notable instances. First, when the gene is found on more than one chromosome (or unplaced scaffold thereof), ...
written 3 days ago by James W. MacDonald42k
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Answer: A: how to transform a list of IRanges into a RangesList instance
... It's just as one might imagine: > lst <- list(IRanges(3,5), IRanges(4,5), IRanges(3,6)) > lst [[1]] IRanges object with 1 range and 0 metadata columns: start end width <integer> <integer> <integer> [1] 3 5 3 [[2]] IRan ...
written 3 days ago by James W. MacDonald42k
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Comment: C: How to analyse clariom d human files
... Yes, that's fine. It's just telling you that some of the probesets map to multiple things. By default you only get one of the multiple mapped IDs. You can for example get all of the multiple mapped IDs, but in practice is easier to just go with the defaults. ...
written 5 days ago by James W. MacDonald42k
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Comment: C: understanding topGO enrichment
... If you want help, and in particular if you are implying that there is a bug (which is what you are doing), it's incumbent upon you to provide a small, self contained example that other people can run to show what you are seeing. In addition, you need to show the results of running sessionInfo(). ...
written 6 days ago by James W. MacDonald42k
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Comment: C: How are feasible genes determined in topGO
... Well, I don't know what to tell you. I say what it means, and you tell me I am wrong, without any evidence as to why I am wrong, and even after you say you can't figure it out yourself. So I'll give you an example to show why I am right and you are wrong, and if you don't believe me, that's cool. B ...
written 6 days ago by James W. MacDonald42k
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Answer: A: How to analyse clariom d human files
... You didn't need to do that at all. You just need to start R in the directory that contains your celfiles and do library(oligo) dat <- read.celfiles(list.celfiles()) eset <- rma(dat) If you then want to add annotations (and who doesn't?), you could use my affycoretools package library(affy ...
written 6 days ago by James W. MacDonald42k
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Answer: A: How to compare 10 GSMxxxxx from one GSE to 10 GSM from another GSE with GEOQuery
... You are doing several things wrong, most of which involve fighting the existing infrastructure that is intended to make your life easier. The data you download are in ExpressionSets, which are fancy ways to encapsulate data in such a way that you can pretend as if they are data.frames that you can ...
written 6 days ago by James W. MacDonald42k
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Comment: C: getBM to retrieve ensembl_gene_id's within a certain distance
... And further to that point: > region2 <- "3:141895564:142895564" > getBM(attributes = "ensembl_gene_id", filters = "chromosomal_region", values = region2, mart = mart.hs) ensembl_gene_id 1 ENSG00000202125 2 ENSG00000200389 3 ENSG00000244124 4 ENSG00000252745 5 ENSG00000120756 6 EN ...
written 6 days ago by James W. MacDonald42k
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Comment: C: getBM to retrieve ensembl_gene_id's within a certain distance
... I should also note that you are assuming that a SNP is actually strand based. It's not. The reference and alternate alleles are different, depending on whichever strand you are talking about, but both strands have either the reference or alternate allele. Genes, on the other hand, are strand based. ...
written 6 days ago by James W. MacDonald42k
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Answer: A: getBM to retrieve ensembl_gene_id's within a certain distance
... > getBM(c("start_position","end_position","strand"), "ensembl_gene_id", "ENSG00000114127", mart.hs) start_position end_position strand 1 142306607 142448062 -1 > region2 <- "3:141895564:142895564:-1" > getBM(attributes = "ensembl_gene_id", filters = "chromosomal_region", ...
written 6 days ago by James W. MacDonald42k

Latest awards to James W. MacDonald

Scholar 3 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 3 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 9 days ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 9 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 4 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
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