Moderator: James W. MacDonald

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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

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Comment: C: oligo and GenericPDInfo
... I don't understand your question. Are you saying that these lines: if (normalize) pm0 <- normalize(pm0, method = "invariantset") run regardless of normalize being TRUE or FALSE? That doesn't seem likely - a bug of that magnitude (e.g., R totally ignoring that if statement) woul ...
written 2 days ago by James W. MacDonald43k
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Answer: A: Returning gene functional annotations with gene symbols as input (using mygene B
... I don't think you need something specific for this. It's just a couple of queries. > library(org.Rn,eg.db) > library(GO.db) ## note that all caps implies human. You want just the first letter capitalized > gns <- c('BRCA1', 'BRCA2', 'SOX2', 'MYC', 'CARNS1') > gns2 <- paste0(subst ...
written 3 days ago by James W. MacDonald43k
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Comment: C: oligo and GenericPDInfo
... There isn't at present much help. The GenericArray infrastructure is supposed to be a generalization of the code to allow things like the MBNI arrays (and any random future Array that Affy might foist upon us) to automatically be accommodated. The old school way of doing things was to take all of A ...
written 3 days ago by James W. MacDonald43k
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Answer: A: oligo and GenericPDInfo
... I don't think there is an easy way to do this (where 'easy' means 'a function exists that you can just use'), particularly since rma has everything hard-coded. But it wouldn't be that hard to roll your own. Something like this? myrma<- function (object, background = TRUE, normalize = TRUE, ...
written 3 days ago by James W. MacDonald43k
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Comment: C: Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
... The complaints arise because the positional information has been moved from the orgDb packages (which are intended to contain mappings of probesets to gene names, symbols, various IDs, etc) to the TxDb packages, which are intended to contain positional information. The ChipDb packages are really jus ...
written 3 days ago by James W. MacDonald43k
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Answer: A: error when trying to apply the specific gene filter.
... Using information about the experiment to filter your data is a horrible idea! The idea behind filtering is to reduce the multiple comparisons by excluding genes that are probably not being expressed, and are just contributing noise and not signal. You can do that by excluding genes with an average ...
written 3 days ago by James W. MacDonald43k
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Comment: C: How to set custom Brainarray annotation for Biobase ExpressionSet object?
... Well, it didn't say that in the code I posted, so your best recourse would be to carefully compare what I did versus what you did, and figure out where you went wrong. ...
written 3 days ago by James W. MacDonald43k
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Answer: A: How to set custom Brainarray annotation for Biobase ExpressionSet object?
... You won't be able to do things that way if you want to use MBNI remapped cdfs. The ae2bioc function is hard-coded to get the Bioconductor pdInfo package for the respective array types. But you can get around it... > aeData = getAE("E-GEOD-14722", type = 'raw') > install.packages("http://mbn ...
written 6 days ago by James W. MacDonald43k
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Answer: A: RSQLite reverse dependencies
... This issue is due to a problem with the NAMESPACE for affycoretools (and oligoClasses as well), where both packages are importing dbGetQuery from RSQLite, rather than the DBI package. The function is defined in DBI and is imported and then exported by RSQLite, and importing the function from RSQLite ...
written 6 days ago by James W. MacDonald43k
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Answer: A: Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
... As Christian noted, the oligo package is the successor to affy, and intended to be used to analyze the newer random-primer arrays. The default for rma in oligo for these arrays is to summarize the core probesets at the transcript level, so dat <- read.celfiles(list.celfiles()) eset <- rma(da ...
written 6 days ago by James W. MacDonald43k

Latest awards to James W. MacDonald

Scholar 5 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 6 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 6 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 9 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 12 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 3 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 3 months ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 3 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 4 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 4 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 4 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 4 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 4 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 4 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?

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