Moderator: James W. MacDonald

Reputation:
48,280
Status:
Trusted
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
6 hours ago
Joined:
16 years, 6 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 • 5,606 results • page 1 of 561 • next >
0
votes
1
answers
61
views
1
answers
Comment: C: Methylation data visualization using methyAnalysis with minfi
... Why do you need a MethyGenoSet to visualize your data? What exactly does 'visualize' mean in this context? ...
written 9 hours ago by James W. MacDonald48k
0
votes
1
answers
38
views
1
answers
Comment: C: Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.kno
... An alternative to that is to generate a fake transcript that consists of the full extent of all known exons. The obvious tradeoff being that in your method you are saying 'this is the important transcript' and in my method you are saying 'these are all the genomic regions that can be part of any tra ...
written 9 hours ago by James W. MacDonald48k
0
votes
1
answers
36
views
1
answers
Answer: A: Help with multi-factored RNA-seq edgeR model
... See section 3.3 of the edgeR User's Guide. ...
written 1 day ago by James W. MacDonald48k
0
votes
0
answers
26
views
0
answers
Comment: C: Small problem of legend color in PCA, is it a bug or a my script miswriting ?
... Hello David ROUX! We believe that this post does not fit the main topic of this site. Questions about ggplot2 should be asked either in R-help or on the tidyverse help (if there is such a thing). For this reason we have closed your question. This allows us to keep the site focused on the topics ...
written 1 day ago by James W. MacDonald48k
0
votes
1
answers
38
views
1
answers
Comment: C: Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.kno
... Also, why do you think that two overlapping exons should only be counted as one? If they have different lengths, they are different, no? ...
written 1 day ago by James W. MacDonald48k
0
votes
1
answers
38
views
1
answers
Answer: A: Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.kno
... We just process the data available at UCSC for these packages, so any errors are theirs not ours. But to check... > library(RMySQL) Loading required package: DBI > con <- dbConnect(MySQL(), user = "genome", host = "genome-mysql.soe.ucsc.edu", dbname="hg19") > library(TxDb.Hsapiens.UCSC ...
written 1 day ago by James W. MacDonald48k
0
votes
2
answers
86
views
2
answers
Comment: C: Importing VCFs in seqCAT
... It looks like the depth information does exist in the mutect, but it's in the INFO column, rather than being defined in the FORMAT column, and then being presented in the individual sample columns, which doesn't make any sense to me, as the depth information is sample-specific rather than allele-spe ...
written 2 days ago by James W. MacDonald48k
0
votes
2
answers
86
views
2
answers
Comment: C: Importing VCFs in seqCAT
... According to VariantAnnotation that's not correct. > z <- readVcf("mutect2_T2_CTL_CTL_rep1_vs_T0_CTL_CTL_rep1_snpEff_VEP.ann.filtered.vcf") Warning messages: 1: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames 2: In .bcfHeaderAsSimpleList(heade ...
written 3 days ago by James W. MacDonald48k
0
votes
2
answers
86
views
2
answers
Comment: C: Importing VCFs in seqCAT
... You should probably be a bit more careful with your terminology and/or understanding of what R is telling you. The error for every failure you have had has been identical - when create_profile is filtering your data, you end up with no data remaining. This error is reflected in the error message: ...
written 3 days ago by James W. MacDonald48k
0
votes
2
answers
86
views
2
answers
Answer: A: Importing VCFs in seqCAT
... The FILTER column in (at least the VCF I looked at) are all missing, and create_profile filters on those that are 'PASS', so after that filtering step you have no remaining data. You probably need to figure out how to get Sarek to put something useful in the FILTER column of your VCF. ...
written 3 days ago by James W. MacDonald48k

Latest awards to James W. MacDonald

Scholar 6 weeks ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Probe to gene id conversion
Teacher 6 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
Scholar 6 weeks ago, created an answer that has been accepted. For A: BiomaRt returns 0 obs
Scholar 6 weeks ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
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: goseq: Formatting category list for use with goseq
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Scholar 11 weeks ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 3 months ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 3 months ago, created an answer that has been accepted. For A: BiomaRt returns 0 obs
Good Answer 3 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 3 months ago, created an answer with at least 3 up-votes. For A: Retrieving all genes related a go term
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: EdgeR blocking and "All combinations of multiple factors"
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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Commentator 3 months 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: goseq: Formatting category list for use with goseq
Teacher 3 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
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: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 166 users visited in the last hour