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

<prev • 5,315 results • page 2 of 532 • next >
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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 7 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 7 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 7 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 8 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 8 days ago by James W. MacDonald46k
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Answer: A: Genes listed in GO categories
... You are, in situation #1, asking for all the Entrez Gene IDs that are associated with a given GO term. And in situation #2 you are asking for all the Ensembl Gene IDs that are associated with a given GO term. These are not the same thing! If you ask two different groups the same question you shouldn ...
written 9 days ago by James W. MacDonald46k
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Answer: A: Annotating Expression Set for GSVA w/ Brainarray Human Gene 1.1 ST Array CDF
... You are doing a bunch of things that don't make sense. First, the data you get from GEO using getGEO is already summarized using the MBNI re-mapped probesets that you want to use. So there is no reason to re-do that part. In addition, the MBNI re-mapped probesets that the original authors used are b ...
written 9 days ago by James W. MacDonald46k
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Comment: C: How i can get a list of KEGG pathways and its list of genes?
... If you have two data.frames with the same things in both, it's trivial to match those up. See e.g., ?match ...
written 9 days ago by James W. MacDonald46k
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Comment: C: How to access normalized data in the NanoStringDiff package?
... That error comes from some checking in sweep to make sure that the length of lambda_i is reasonable for the dimensions of the matrix you are sweeping on. So there appears to be a problem with either your Y matrix or whatever you are getting for lambda_i. You need to take a look at those data and see ...
written 13 days ago by James W. MacDonald46k
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Answer: A: How to access normalized data in the NanoStringDiff package?
... I don't think there is a direct accessor, but this is what is done to the data prior to fitting any model: c = positiveFactor(NanoStringData) d = housekeepingFactor(NanoStringData) k = c * d lamda_i = negativeFactor(NanoStringData) Y = exprs(NanoStringData) Y_n = sweep(Y, 2 ...
written 13 days ago by James W. MacDonald46k

Latest awards to James W. MacDonald

Scholar 5 weeks ago, created an answer that has been accepted. For A: Bioconductor: quantile normalization
Scholar 5 weeks ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Teacher 5 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 5 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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