Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 20k
Reputation:
19,570
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United States
Website:
http://bioconductor.org/
Last seen:
4 hours ago
Joined:
11 years, 7 months ago
Email:
m************@roswellpark.org

Posts by Martin Morgan

<prev • 2,476 results • page 1 of 248 • next >
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Comment: C: package "isa2", function isa.iterate()
... Since the generic is not exported, showMethods() needs to be told where to look > showMethods("isa.iterate", where=getNamespace("isa2")) Function: isa.iterate (package isa2) normed.data="list" A convenient way to get source code for methods when there are only one or two is to use the argument ...
written 5 hours ago by Martin Morgan ♦♦ 20k
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Comment: C: Rsamtools fetch MD:Z field from bam files
... There is a typo in your call to ScanBamParam -- pram= instead of param=. For the system file, there is no record with the MD tag, so no way for R to know what type of vector to allocate for it, hence NULL. ...
written 1 day ago by Martin Morgan ♦♦ 20k
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Comment: C: BioC 2017: Where Software and Biology Connect, 26 / 27 - 28 July, Boston, MA
... Expect developer day lightning talk sign-up several weeks before the conference, on the conference web site. Scholarship housing is usually arranged by us at one of the conference hotels; scholarship recipients should be informed by the end of this week. ...
written 2 days ago by Martin Morgan ♦♦ 20k
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Answer: A: Rsamtools fetch MD:Z field from bam files
... Are ScanBamParam() arguments tag and tagFilter what you are looking for? See ?ScanBamParam. ...
written 2 days ago by Martin Morgan ♦♦ 20k
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Comment: C: RankProd crashing - stability issues?
... When I try and reproduce your code, I run into the following problem, for obvious reasons > norm <- read.delim("norm.txt", header=T) Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'norm.txt': No such file or direc ...
written 5 days ago by Martin Morgan ♦♦ 20k
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Comment: C: RankProd crashing - stability issues?
... You need to show us how you produce the problem -- a few lines of code that I can copy and paste into my own session and see what happens. You need to be using the current version of Bioconductor (R version 3.4.0, BiocInstaller version 1.26.0). It looks like you have an old version of R and RankProd ...
written 6 days ago by Martin Morgan ♦♦ 20k
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Answer: A: TarSeqQC TargetExperiment() Error- failed to stop SOCKcluster cluster-error writ
... This may indicate an error trying to move too much data from the worker back to the master; you could try BiocParallel::register(BiocParallel::SerialParam()) before the call to TargetExperiment() to run in serial mode. ...
written 7 days ago by Martin Morgan ♦♦ 20k
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Comment: C: RankProd crashing - stability issues?
... These types of question usually require a simple reproducible example, and information about the specific software you use. Please update your question to (a) include a reproducible example, e.g., using a data set from RankProd or simple simulated data and (b) include the output of the sessionInfo() ...
written 7 days ago by Martin Morgan ♦♦ 20k
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Comment: C: Problem with upgrading Bioconductor from 3.4 to 3.5
... It was only necessary to remove the BiocInstaller package, not all R / all packages, but I'm glad you got it working. ...
written 8 days ago by Martin Morgan ♦♦ 20k
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Answer: A: Problem with upgrading Bioconductor from 3.4 to 3.5
... Remove (all copies of) BiocInstaller and source("https://bioconductor.org/biocLite.R"). This should provide you with BiocInstaller version 1.26.0; use biocValid() and biocLite(ask=FALSE) to update packages. ...
written 8 days ago by Martin Morgan ♦♦ 20k

Latest awards to Martin Morgan

Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Scholar 13 days ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Scholar 13 days ago, created an answer that has been accepted. For A: BiocParallel: messages shown only when processes finished
Scholar 22 days ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 23 days ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 29 days ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Appreciated 4 weeks ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 5 weeks ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 5 weeks ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 8 weeks ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Appreciated 9 weeks ago, created a post with more than 5 votes. For BioC 2015 Annual Conference
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 10 weeks ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 11 weeks ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 11 weeks ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Appreciated 3 months ago, created a post with more than 5 votes. For BioC 2015 Annual Conference
Scholar 3 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 3 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: about the use of subsetByFilter()
Scholar 3 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Scholar 4 months ago, created an answer that has been accepted. For A: about the use of subsetByFilter()
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: bplapply stalling upon error with large data objects

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