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 • 4,511 results • page 2 of 452 • next >
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Comment: C: How to use brainarray custom cdf with oligo package?
... There are two problems here. First, you are confusing things; the instructions above are for making a pdInfoPackage, which isn't an annotation package. Instead, it is a package that oligo uses to map probes to probesets so you can summarize your data. Second, you don't need to make these any more, a ...
written 5 days ago by James W. MacDonald41k
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Answer: A: Error in BSGenome "getSeq" function
... It looks like it might be something local to your installation. > dnaseq <- getSeq(BSgenome.Dmelanogaster.UCSC.dm6) > dnaseq A DNAStringSet instance of length 1870 width seq names [1] 23513712 CGACAATGCACGACAGAGGA...GAA ...
written 6 days ago by James W. MacDonald41k
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Comment: C: Annotating DEseq output using AnnotationDbi mapIds and most results say NA
... If you want more recent transcripts, you need to use a more recent version of the Ensembl database. The version that Johannes provides is based on Ensembl V79 (hence the v79 in the name), which is rather old. Biomart is based on the current version: > ids <- paste0("ENSMUST00000", c(195892, ...
written 7 days ago by James W. MacDonald41k
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Answer: A: Annotating DEseq output using AnnotationDbi mapIds and most results say NA
... The org.Mm.eg.db package is based on NCBI annotations, whereas you are trying to annotate using Ensembl IDs. Trying to use one annotation source to annotate another is a recipe for heartache, for a number of reasons. You will be better off just using Ensembl databases to do the mapping. You can do t ...
written 7 days ago by James W. MacDonald41k
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Comment: C: Duplicate gene ID's returned from limma microarray analysis
... You might also consider using getMainProbes. The two probesets with identical results (13282364 and 13284182) are made up of the same probes, which is why the results are identical. But both probesets are so-called 'rescue' probesets that are, um, used to rescue things and whatnot. There are any nu ...
written 7 days ago by James W. MacDonald41k
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Comment: C: TopGO code Line
... You will unfortunately never get any help for a question like that, as it is completely uninterpretable. What exactly is the difference between GO:000..X and GO:000...Y? What do those two things even mean? You will probably be much better off if you just simply state what you are trying to do, and ...
written 8 days ago by James W. MacDonald41k
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Answer: A: adding attributes affects number of results returned
... A good rule of thumb is to try doing a similar query at the Ensembl Biomart site if it fails within biomaRt. When I try that, I can make a query for everything but the associated gene (same as in biomaRt). But when I add in the associated_gene (which if you check listAttributes is the 'Associated ge ...
written 8 days ago by James W. MacDonald41k
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Answer: A: bumphunter output clarification: p values achieved with b=1000: further correcti
... When you permute (or draw bootstraps) you are trying to estimate the null distribution for each bump and are then comparing your observed value to the null distribution. A p-value estimates the probability of getting your observed result (or larger) under the null distribution, and when you permute ...
written 11 days ago by James W. MacDonald41k
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Answer: A: perform probe level RMA without summarization
... It's not clear exactly what you are after; I assume you just want to background correct and then normalize the probes? You can easily do that. As an example: > dat <- ReadAffy() > dat AffyBatch object size of arrays=712x712 features (18 kb) cdf=HG-U133A (22283 affyids) number of samples= ...
written 11 days ago by James W. MacDonald41k
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Comment: C: problem with makeOrgPackageFromNCBI when making an annotation package
... It is not ideal to add onto a months-old thread. Instead you should consider starting a new thread, even if your question is related. In addition, the box below, labeled 'Add your answer' is not intended for you to add another question, nor to add a comment; as the title suggests, it's for adding an ...
written 11 days ago by James W. MacDonald41k

Latest awards to James W. MacDonald

Scholar 9 months ago, created an answer that has been accepted. For A: toTable(org.Dr.egGO) into a data.frame with unique gene_id and all ensembl_ids i
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to compare result of fisher.test() with another numeric value in R ?
Scholar 9 months ago, created an answer that has been accepted. For A: toTable(org.Dr.egGO) into a data.frame with unique gene_id and all ensembl_ids i
Scholar 9 months ago, created an answer that has been accepted. For A: toTable(org.Dr.egGO) into a data.frame with unique gene_id and all ensembl_ids i
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to compare result of fisher.test() with another numeric value in R ?
Scholar 9 months ago, created an answer that has been accepted. For A: toTable(org.Dr.egGO) into a data.frame with unique gene_id and all ensembl_ids i
Scholar 9 months ago, created an answer that has been accepted. For A: toTable(org.Dr.egGO) into a data.frame with unique gene_id and all ensembl_ids i
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to compare result of fisher.test() with another numeric value in R ?
Scholar 10 months ago, created an answer that has been accepted. For A: toTable(org.Dr.egGO) into a data.frame with unique gene_id and all ensembl_ids i
Scholar 10 months ago, created an answer that has been accepted. For A: toTable(org.Dr.egGO) into a data.frame with unique gene_id and all ensembl_ids i
Scholar 10 months ago, created an answer that has been accepted. For A: How to compare result of fisher.test() with another numeric value in R ?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to compare result of fisher.test() with another numeric value in R ?
Scholar 11 months ago, created an answer that has been accepted. For A: TxDb.Hsapiens.UCSC.hg19.knownGene Exons that are not part of any gene
Scholar 11 months ago, created an answer that has been accepted. For A: How to compare result of fisher.test() with another numeric value in R ?
Scholar 11 months ago, created an answer that has been accepted. For A: How to compare result of fisher.test() with another numeric value in R ?
Appreciated 11 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 11 months ago, created an answer that has been accepted. For A: How to compare result of fisher.test() with another numeric value in R ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to compare result of fisher.test() with another numeric value in R ?
Scholar 11 months ago, created an answer that has been accepted. For A: How to compare result of fisher.test() with another numeric value in R ?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Error: This function only works when used with the ensembl BioMart.
Scholar 11 months ago, created an answer that has been accepted. For A: TxDb.Hsapiens.UCSC.hg19.knownGene Exons that are not part of any gene
Scholar 11 months ago, created an answer that has been accepted. For A: TxDb.Hsapiens.UCSC.hg19.knownGene Exons that are not part of any gene
Scholar 11 months ago, created an answer that has been accepted. For A: Error: This function only works when used with the ensembl BioMart.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Error: This function only works when used with the ensembl BioMart.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Error: This function only works when used with the ensembl BioMart.

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