User: Wacek Kusnierczyk

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Posts by Wacek Kusnierczyk

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Comment: C: GO.db: how to get GO Term
... Interesting, thanks. vQ > Hi Gordon, Martin, Wacek, > > Martin Morgan wrote: >> Wacek Kusnierczyk wrote: >>> Marc Carlson wrote: >>>> One thing you can do to make this more efficient is to use mget >>>> instead >>>> of as.list(). That wa ...
written 8.4 years ago by Wacek Kusnierczyk180
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Comment: C: GO.db: how to get GO Term
... Marc Carlson wrote: > One thing you can do to make this more efficient is to use mget instead > of as.list(). That way you won't be pulling the whole mapping out of > the database into a list just to get one thing back out. > > mget("GO:0000166",GOTERM,ifnotfound=NA) > > Also, ...
written 8.4 years ago by Wacek Kusnierczyk180
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Answer: A: GO.db: how to get GO Term
... Gordon K Smyth wrote: > What is the recommended way to find the GO term that corresponds to a > given GO accession number? I can do this: > > > library(GO.db) > > Term(as.list(GOTERM["GO:0000166"])[[1]]) > [1] "nucleotide binding" > > But this seems a bit inelega ...
written 8.4 years ago by Wacek Kusnierczyk180
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Answer: A: miRNA and validated/predicted target genes
... mauede at alice.it wrote: > I posted the following question to R mailing-list and was adviced to contact the BioConductors team. > > I have to find humans miRNA sequences and the correspondent validated and/or predicted gene sequences. > The only database I know of is http://mirecords.u ...
written 8.4 years ago by Wacek Kusnierczyk180
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Comment: C: GEOquery and parsing SOFT files
... Sean Davis wrote: > On Tue, May 26, 2009 at 3:21 AM, Wacek Kusnierczyk < > Waclaw.Marcin.Kusnierczyk at idi.ntnu.no> wrote: > > >> Sean Davis wrote: >> >> [...] >> >>> Thanks, Wacek, for the report. This is a known issue and GEOquery could >> ...
written 8.5 years ago by Wacek Kusnierczyk180
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Comment: C: GEOquery and parsing SOFT files
... Sean Davis wrote: [...] > Thanks, Wacek, for the report. This is a known issue and GEOquery could > probably be smarter than it currently is; I have not changed that code in q > while since GEO began using GSE Matrix files. You could try using > GSEMatrix=TRUE, as the documentation su ...
written 8.5 years ago by Wacek Kusnierczyk180
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Comment: C: GEOquery and parsing SOFT files
... Wolfgang Huber wrote: > > Dear Wacek, > > thank you for the feedback and pointing this out. Two general remarks: thank you for the response. > > 1. Please include a reproducible example (R script) for others to > reproduce your experience, and subsequently the output of sessio ...
written 8.5 years ago by Wacek Kusnierczyk180
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GEOquery and parsing SOFT files
... Hello, The getGEO function from GEOquery parses GEO soft files. With a particular GSE file (GSE13638), it took over 15 minutes on my not-so-crappy machine to parse the file (a local file, download time excluded). I've written a simple parser in perl, and parsing the same file and storing the data ...
geoquery written 8.5 years ago by Wacek Kusnierczyk180 • updated 8.5 years ago by Wolfgang Huber13k
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Comment: C: mislinked task views?
... Vincent Carey wrote: > It is true that the biocViews/inst/dot/biocViewsVocab.dot indicates two > paths to > BiologicalDomains (via Software and ExperimentData). For consistent HTML > generation such a structure should probably not be allowed. > > it's not a problem of html genera ...
written 8.5 years ago by Wacek Kusnierczyk180
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mislinked task views?
... hello, there is a minor problem with links in the hierarchy of tasks at bioc views [1]. the top category is subdivided into software, annotation data, and experiment data. clicking on software/biological domains leads to a task view where the are no packages, and the parent category is experiment ...
cancer category written 8.5 years ago by Wacek Kusnierczyk180 • updated 8.5 years ago by Vincent J. Carey, Jr.6.2k

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