Moderator: James W. MacDonald

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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: Understaning of two-color array data
... Hello firoz.imtech! We believe that this post does not fit the main topic of this site. This site is intended to support Bioconductor packages, not GEO. You might consider contacting the submitter of those data. For this reason we have closed your question. This allows us to keep the site focuse ...
written 1 hour ago by James W. MacDonald46k
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Comment: C: Genes listed in GO categories
... No, I am not saying that mapping across services is never a sensible thing to do. What I am saying is that it is a non-trivial thing to do, because it may have unexpected consequences. For example, in the original post to this thread the OP states that the Ensembl mappings for that GO term were for ...
written 2 days ago by James W. MacDonald46k
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Answer: A: GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
... There appears to be an issue with an internal function that may need to be addressed. But you probably don't need to build your own TxDb; you can get comparable objects from AnnotationHub with much less fuss: > library(AnnotationHub) > hub <- AnnotationHub() snapshotDate(): 2018-04-30 &g ...
written 2 days ago by James W. MacDonald46k
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Comment: C: Annotating Expression Set for GSVA w/ Brainarray Human Gene 1.1 ST Array CDF
... I am not sure what you mean by 'redoing the mappings'. In my mind a mapping is usually from a manufacturer's ID to an ID from an annotation service like NCBI or EBI/EMBL. However you might actually mean 'redoing the normalization and summarization steps', in which case you should note that oligo doe ...
written 3 days ago by James W. MacDonald46k
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Comment: C: Genes listed in GO categories
... I think that's correct. Thanks for pointing that out. The only real issue here (IMO) then is that Ensembl IDs will be silently converted to Gene IDs to do the GO mapping if a gene2cat data.frame isn't supplied. IMO this is a fraught process! The OP has already documented that EBI/EMBL have quite dif ...
written 4 days ago by James W. MacDonald46k
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Comment: C: Merging each element of a list of Genomic range
... Thinking about this further, I am not sure my nor Michael's answer is 100% correct. For example, there is SAMD11, which has many transcripts: > samd11 <- select(TxDb.Hsapiens.UCSC.hg19.knownGene, "148398", "TXNAME","GENEID") 'select()' returned 1:many mapping between keys and columns > sa ...
written 5 days ago by James W. MacDonald46k
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Answer: A: Merging each element of a list of Genomic range
... It's not exactly clear what you mean by 'to get the first and last possible CDS GRanges'. That could be interpreted as wanting at most two GRanges per CDS, or what I assume you actually want, which would be to get a single GRanges item for each CDS that extends to the furthest extent of any underlyi ...
written 5 days ago by James W. MacDonald46k
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Comment: C: trying to reproduce heat map made via cBioportal using download data
... Hello chrisclarkson100! We believe that this post does not fit the main topic of this site. This question doesn't have anything to do with any Bioconductor package, and is instead a general question about how to analyze data from cbioportal. You should ask them. For this reason we have closed yo ...
written 5 days ago by James W. MacDonald46k
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Answer: A: Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent fi
... The targets file is often something you need to construct. Examples can be found in section 4.3 of the limma User's Guide. All of the files (other than the first two) that you list contain raw data. The Readme file (which you should read) contains phenotypic information about the samples hybridized ...
written 5 days ago by James W. MacDonald46k
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Comment: C: Genes listed in GO categories
... The argument isn't 'ensGene', that's the input for the 'genes' argument, which tells goseq what sort of ID you are using. If the OP were using Entrez Gene IDs, then the argument would be 'knownGene'. The genome has very little to do with this, other than for getting the gene lengths. In my mind, an ...
written 6 days ago by James W. MacDonald46k

Latest awards to James W. MacDonald

Scholar 4 weeks ago, created an answer that has been accepted. For A: Bioconductor: quantile normalization
Scholar 4 weeks ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Teacher 4 weeks 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 weeks ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Strong upwards correlation between log fold change and average log expression in
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Error in Gviz | IdeogramTrack
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: how to extract Granges not overlapping with other ganges?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Best way to convert uniprot accessions to entrez gene identifiers in R
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: limma - F-test for many condition
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: how to transform a list of IRanges into a RangesList instance
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: including information indicating upregulation/downregulation of genes in goana()
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Voom: estimation of mean-variance relationship with gene expression data normali
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: package ‘edgeR’ is not available (for R version 3.1.2)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Why do I get different GO term sizes using the same gene universe for 2 analyses
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: featureCounts in-built annotation doesn't match BioMart annotation?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Glimma Interactive plots for RNAseq
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Interpretation of voom limma's intercept coefficient
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Finding gene lengths of mm10 to calculate rpkm grom count matrix of rna-seq data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to deal with Affymetrix GeneChip probeids that map to multiple genes
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Unable to install a Bioconductor package to local directory
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Agilent microarray chip normalization/background correction
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Identify up and down regulated genes in affymetrix data

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