Moderator: James W. MacDonald

Reputation:
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Location:
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Joined:
16 years, 11 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 • 5,829 results • page 2 of 583 • next >
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Answer: A: edgeR and batch effect correction for differential analysis
... Use the `DGEList` object and include the batch effect in your model. ...
written 5 days ago by James W. MacDonald50k
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Comment: C: edgeR removing batch effect before using expression data for clustering
... No, it's not wrong, particularly if you are doing MDS, which is what he is talking about in that post. There is never any mention of heatmaps, and only the OP is talking about PCA. And Gordon specifically mentions that he isn't enthused with using the scale argument to `prcomp`, and I would interpre ...
written 5 days ago by James W. MacDonald50k
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Comment: C: edgeR removing batch effect before using expression data for clustering
... Did you read my answer? ...
written 5 days ago by James W. MacDonald50k
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Answer: A: error on ReadAffry for CEL file
... You are mixing up installers. And we are on R-3.6.0 now, so install R-3.6.0, then do ``` install.packages("BiocManager") library(BiocManager) install("affy") library(affy) affy_obj <- ReadAffy() ``` and let us know how it goes. ...
written 5 days ago by James W. MacDonald50k
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Answer: A: edgeR removing batch effect before using expression data for clustering
... You should run `removeBatchEffect` after computing logCPM, but you should probably use `voom` rather than `cpm` for that step. The difference being that `voom` will also generate observation-level weights that will be passed to `lmFit` for the batch correction. ...
written 6 days ago by James W. MacDonald50k
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Comment: C: Annotation of Rice Affymatrix Data
... It's not absent. You have evidently removed it. ``` > z <- getGEO("GSE49242") Found 1 file(s) GSE49242_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49242/matrix/GSE49242_series_matrix.txt.gz' Content type 'application/x-gzip' length 3219347 bytes (3.1 M ...
written 7 days ago by James W. MacDonald50k
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Comment: C: How to construct a subset of TxDb object from TxDb.Hsapiens.UCSC.hg38.knownGene
... You won't save any time by doing that. It will take way more time to generate the subsetted TxDb package than it would take to simply run `annotatePeak` on the whole thing, even if you have to run `annotatePeak` multiple times. Don't try to save pennies by spending dollars. ...
written 10 days ago by James W. MacDonald50k
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Comment: C: Help creating VRange object
... Yes, that works in this instance, where the DNAStringSetList for the ALT allele has only one allele per position. But if that isn't true, then it doesn't work ``` > z <- vcfRange$ALT > z[1] <- DNAStringSetList(c("G", "T")) > vcfRange$ALT <- z > test_range=VRanges( seqnames = ...
written 10 days ago by James W. MacDonald50k
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Comment: C: Brainarray CDF with oligopackage
... Your first post no longer makes sense to me. Do you want the mapping to be based on Ensembl (hence ense in the name) or NCBI (hence entrezg in the name)? If you want NCBI IDs, then you need to install from 'http://mbni.org/customcdf/23.0.0/entrezg.download/pd.mogene21st.mm.entrezg_23.0.0.tar.gz'. I ...
written 10 days ago by James W. MacDonald50k
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Answer: A: Brainarray CDF with oligopackage
... MBNI now builds pdInfoPackages that you can use directly. ``` > install.packages("http://mbni.org/customcdf/23.0.0/ense.download/pd.mogene21st.mm.ense_23.0.0.tar.gz", repos = NULL, type = "source") Installing package into 'C:/Users/jmacdon/AppData/Roaming/R/win-library/3.5' (as 'lib' is unspecif ...
written 10 days ago by James W. MacDonald50k

Latest awards to James W. MacDonald

Scholar 4 months ago, created an answer that has been accepted. For A: Retrieving all genes related a go term
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to export enrichGO results for future visualization with barplot, dotplot, e
Teacher 4 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
Teacher 4 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 4 months ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Scholar 4 months ago, created an answer that has been accepted. For A: IRanges which are not S4 generic: endoapply mendoapply error in loading oligocla
Scholar 4 months ago, created an answer that has been accepted. For A: Correct usage of tximport counts in edgeR without offset matrix.
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Best way to convert uniprot accessions to entrez gene identifiers in R
Scholar 4 months ago, created an answer that has been accepted. For A: Iterate through sever annotation database packages
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 4 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 4 months ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 4 months ago, created an answer that has been accepted. For A: Probe to gene id conversion
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Conduct likelihood ratio tests for a variable that isn't explicitly defined by m
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: HTA 2.0 Differential expression analysis - design question
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Probe to gene id conversion
Scholar 4 months ago, created an answer that has been accepted. For A: Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens
Scholar 4 months ago, created an answer that has been accepted. For A: How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: EdgeR blocking and "All combinations of multiple factors"
Scholar 4 months ago, created an answer that has been accepted. For A: limma - blocking or regressing out nuisance variable
Scholar 4 months ago, created an answer that has been accepted. For A: Problems with "exonsBy" function from GenomicFeatures package
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Different annotation obtained from hgu133a2.db and affymetrix annotation release
Scholar 4 months ago, created an answer that has been accepted. For A: Bioconductor: quantile normalization
Scholar 4 months ago, created an answer that has been accepted. For A: Human Exon: arome.affymetrix residuals Inf value

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