Moderator: James W. MacDonald

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Last seen:
21 hours ago
Joined:
16 years, 2 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 • 5,413 results • page 2 of 542 • next >
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Answer: A: Design Matrix with paired and independent samples plus RUVg Spike-in normalizati
... I don't see how you can do that in one go using a fixed effect for patient. You can't fit a patient level blocking factor if you have some patients with just one observation, and the comparisons between the pre-treatment and controls and the post-treatment and controls don't involve any repeated mea ...
written 3 days ago by James W. MacDonald47k
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Comment: C: Help with Censoring using the survival package.
... Hello Ahdee! We believe that this post does not fit the main topic of this site. Survival is a base R package, not Bioconductor. Please ask at r-help@r-project.org For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with ...
written 4 days ago by James W. MacDonald47k
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Answer: A: numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
... There are two things going on here. First, the Gene Ontology (GO) is set up as a directed acyclic graph, which simply means that we start at the highest, most general level (e.g., Biological Process), and then keep splitting into more specific terms. By default, since all of the lower GO terms are m ...
written 4 days ago by James W. MacDonald47k
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Comment: C: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... 2.) Not really. It attaches the two databases and then does an inner join query between the tables. But I am not sure you would get any different results if you did the two-step procedure you outline. 3.) The two files are different because Affy goes back on a semi-regular basis and ensures that th ...
written 4 days ago by James W. MacDonald47k
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Answer: A: Filtering the expression values of a gene from GEO
... library(GEOquery) gse <- getGEO("GSE20966")[[1]] pData(gse)[,"disease.ch1"] ...
written 4 days ago by James W. MacDonald47k
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Comment: C: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... 1.) Yes, mget is old tech as well. Use either select or mapIds. If you are just trying to annotate an ExpressionSet, you might consider using annotateEset from my affycoretools package. Why exactly are you using data.table? I can't imagine that is particularly useful in this context (where by 'this ...
written 4 days ago by James W. MacDonald47k
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Comment: C: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... Or if you just want the RefSeq ID: select(ragene20sttranscriptcluster.db, "17610996", "REFSEQ") 'select()' returned 1:many mapping between keys and columns PROBEID REFSEQ 1 17610996 NM_019370 2 17610996 NP_062243 3 17610996 XM_008758654 4 17610996 XP_008756876   ...
written 5 days ago by James W. MacDonald47k
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Answer: A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
... The answer is a bit more complicated than what you might think. First, using the old BiMap interface (e.g., using things like ragene20sttranscriptclusterCHR directly) is probably suboptimal at this point, and you should be using either select or mapIds instead. Second, these days the ChipDb objects ...
written 5 days ago by James W. MacDonald47k
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Answer: A: Installing GEOQuery failed with conda
... Did you see this part? ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libxml-2.0 was not found. Try installing: * deb: libxml2-dev (Debian, Ubuntu, etc) * rpm: libxml2-devel (Fedora, CentOS, RHEL) * csw: libxml2_dev (Solaris) You need the libx ...
written 5 days ago by James W. MacDonald47k
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Answer: A: SYMBOL is not the official MGI gene symbol?
... The data for the org.Mm.eg.db package is parsed from files we download from NCBI. One of which is the gene_info.gz file. If I download that file and look for that Gene ID, this is what I get: zcat gene_info.gz | awk '{if(NR == 1 || ($1 == 10090 && $2 == 17711)) print $2"\t"$3}' GeneID Sym ...
written 5 days ago by James W. MacDonald47k

Latest awards to James W. MacDonald

Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Best way to convert uniprot accessions to entrez gene identifiers in R
Scholar 11 weeks ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Scholar 11 weeks ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For GEOquery error
Teacher 11 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
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Retrieving all genes related a go term
Commentator 11 weeks 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
Scholar 3 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Scholar 3 months ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Scholar 3 months ago, created an answer that has been accepted. For A: Bioconductor: quantile normalization
Teacher 3 months 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 3 months ago, created an answer that has been accepted. For A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
Teacher 13 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 13 months ago, created an answer with at least 3 up-votes. For A: including information indicating upregulation/downregulation of genes in goana()
Teacher 13 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 13 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 13 months ago, created an answer with at least 3 up-votes. For A: limma - F-test for many condition
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Error in Gviz | IdeogramTrack
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: how to extract Granges not overlapping with other ganges?
Teacher 13 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 13 months ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Unable to install a Bioconductor package to local directory
Teacher 13 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 13 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

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