Moderator: James W. MacDonald

Reputation:
41,380
Status:
Trusted
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
8 hours ago
Joined:
14 years, 7 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 • 4,516 results • page 1 of 452 • next >
0
votes
0
answers
65
views
0
answers
Comment: C: topGO: No adjacent nodes prevents BP analysis
... You will need to provide a self-contained, reproducible example that people can use to test. Another alternative is to use the GOstats package, or the goana function in limma. ...
written 1 day ago by James W. MacDonald41k
0
votes
2
answers
49
views
2
answers
Answer: A: SAM/siggenes: Differential gene expression analysis
... Neither siggenes nor samr can correctly handle technical replicates, as far as I know. If you used the classlabel as you describe then you will consider technical replicates as if they were biological replicates, which all things equal should bias you towards the alternative hypothesis. In other wor ...
written 1 day ago by James W. MacDonald41k
0
votes
1
answers
58
views
1
answers
Answer: A: Gene set Testing with Limma for Agilent IDs probes?
... Running summary on a list is probably not that great an idea, as you doubtless found out. Instead, it's preferable to first find the class of an object and then query from there. > class(Hs.c2) [1] "list" > length(Hs.c2) [1] 4729 > class(Hs.c2[[1]]) [1] "character" > head(Hs.c2[[1]]) [ ...
written 1 day ago by James W. MacDonald41k
0
votes
1
answers
46
views
1
answers
Answer: A: Custom cdf and Ensemble
... The MBNI custom cdfs are generated by a group that is completely distinct from Bioconductor. If you have questions about their cdfs, please ask them, not us. ...
written 1 day ago by James W. MacDonald41k
0
votes
1
answers
48
views
1
answers
Answer: A: Custom cdf files and genes
... The probeset IDs for the MBNI custom cdfs are the database ID concatenated to _st. So e.g., if you were using the Entrez Gene version, given an Entrez Gene ID of 1223, the probeset ID would be 1223_st. If we assume you have run rma to get an ExpressionSet (that you called 'eset'), you can then make ...
written 1 day ago by James W. MacDonald41k
0
votes
3
answers
97
views
3
answers
Answer: A: convert data frame of Entrez IDs to Gene Symbols
... It's just a matter of coercion, isn't it? > myGenes <- data.frame(matrix(c(1572, 1571, 4129, NA, 216, 217, 15, 3620, 7453,NA), 2)) > myGenes X1 X2 X3 X4 X5 1 1572 4129 216 15 7453 2 1571 NA 217 3620 NA > myGenes2 <- data.frame(matrix(mapIds(org.Hs.eg.db, as.charact ...
written 2 days ago by James W. MacDonald41k
0
votes
1
answers
62
views
1
answers
Answer: A: Annotations of custom cdf files
... You can look at the GPL for the array that the submitter chose when submitting the microarray data, which is on the GEO page for the data you are using. ...
written 3 days ago by James W. MacDonald41k
0
votes
2
answers
50
views
2
answers
Answer: A: BioC and genevisR and maftools
... You have a complete mismatch between your Bioconductor and R versions. BioC 3.2 was intended for R-3.2.x You should restart R, then do source("https://www.bioconductor.org/biocLite.R") biocLite() Which should get you the correct version of BiocInstaller, which will then install the correct versi ...
written 6 days ago by James W. MacDonald41k
0
votes
1
answers
73
views
1
answers
Answer: A: error in GenomicFeature
... It's not clear what you are trying to do. Why not just use the existing package for those data? Re-creating an already extant package is a waste of time, I would think. library(BiocInstaller) biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene") library(TxDb.Hsapiens.UCSC.hg38.knownGene) ...
written 6 days ago by James W. MacDonald41k
0
votes
1
answers
61
views
1
answers
Answer: A: Why does a `first_time` object appear when showing GRangesList object?
... This comes from BiocGenerics, in particular the unsafe_replaceSlots function. The code is pretty well commented, so I will point you there for a rationale. ...
written 6 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 12 months ago, created an answer with at least 3 up-votes. For A: Error: This function only works when used with the ensembl BioMart.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 168 users visited in the last hour