Moderator: James W. MacDonald

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51,370
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Location:
United States
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Google Scholar Page
Last seen:
1 day, 2 hours ago
Joined:
17 years, 5 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 • 6,059 results • page 1 of 606 • next >
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Answer: A: Ask for help on the preprocessing of GEO microarray data with Oligo and affy pac
... ``` > library(GEOquery) > getGEOSuppFiles("GSE41418") > setwd("GSE41418/") > untar("GSE41418_RAW.tar") > cels <- dir(".", "CEL.gz$") > library(affy) Bioconductor version 3.10 (BiocManager 1.30.7), ?BiocManager::install for help > install.packages("http://mbni.org/customcdf/2 ...
written 1 day ago by James W. MacDonald51k
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Answer: A: batch correction in DESeq2 > matrix not full rank > mitigate
... The short answer is that you can't do that. There's no way to resolve the confounding. ...
written 1 day ago by James W. MacDonald51k
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Comment: C: crlmm support for Illumina arrays with no annotation package?
... You appear to be getting jammed up at this step: ``` calculateParameters <- function(M, priormeans, numSNP, verbose) { if (verbose) message("Start calculating 3-cluster parameters") params3cluster <- calculateParameters3Cluster(M, priormeans, numSNP, verbose); if (verbose) message ...
written 1 day ago by James W. MacDonald51k
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Comment: C: crlmm support for Illumina arrays with no annotation package?
... What do you get when you do (after loading `crlmm`): ``` crlmm:::getNumberOfCores() ``` ...
written 1 day ago by James W. MacDonald51k
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Comment: C: Why package "BiocLite" is not available (for R version 3.6.1)
... You can even install GitHub packages using `BiocManager::install`, so there really is no reason to use anything else to install packages. ...
written 2 days ago by James W. MacDonald51k
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Comment: C: crlmm support for Illumina arrays with no annotation package?
... Actually, if either of you would do me a favor? [Download the updated version of crlmm][1], and then install by doing ``` install.packages("crlmm_1.45.1.tar.gz", repos = NULL) ``` And then run `genotype.Illumina` as normal and let me know if it works. [1]: https://drive.google.com/open?id=1JLL ...
written 2 days ago by James W. MacDonald51k
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Answer: A: crlmm support for Illumina arrays with no annotation package?
... It looks to me like there is a small bug in `RGtoXY`, which is an internal function that does ``` if (chipType == "nopackage" && !is.null(anno)) { pkgname = NULL if(sum(colnames(anno@data)=="AddressA_ID")!=1){ message("annotation format is wrong, could not fi ...
written 2 days ago by James W. MacDonald51k
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Answer: A: Detecting the power in differential expression
... You might look at [sizepower][1]. [1]: http://bioconductor.org/packages/release/bioc/html/sizepower.html ...
written 2 days ago by James W. MacDonald51k
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Answer: A: Not latest package version through 'BiocManager::install()'
... You don't show the results of `sessionInfo` so it's not possible to help you. Assuming you have an older version of R, you need to update. Do note that we don't provide help for those who download things and install separately. Each release is intended to work, but there are no guarantees that you c ...
written 3 days ago by James W. MacDonald51k
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Answer: A: CRISPR SEEK TxDb issue
... ``` > library(AnnotationHub) > hub <- AnnotationHub() > z <- query(hub, c("sus scrofa","txdb")) > z AnnotationHub with 9 records # snapshotDate(): 2019-10-29 # $dataprovider: UCSC # $species: Sus scrofa # $rdataclass: TxDb # additional mcols(): taxonomyid, genome, description, # ...
written 3 days ago by James W. MacDonald51k

Latest awards to James W. MacDonald

Scholar 3 months ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 3 months ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Appreciated 3 months ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Scholar 10 months ago, created an answer that has been accepted. For A: Limma import .gpr file error
Scholar 10 months ago, created an answer that has been accepted. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Popular Question 10 months ago, created a question with more than 1,000 views. For Saving/loading TxDb objects
Appreciated 10 months ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 10 months ago, created an answer that has been accepted. For A: limma - blocking or regressing out nuisance variable
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 10 months ago, created an answer that has been accepted. For A: Iterate through sever annotation database packages
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Scholar 10 months ago, created an answer that has been accepted. For A: Probe to gene id conversion
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 10 months ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Different annotation obtained from hgu133a2.db and affymetrix annotation release
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 10 months ago, created an answer that has been accepted. For A: Problems with "exonsBy" function from GenomicFeatures package

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