User: Jeff Gentry

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Jeff Gentry3.9k
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Posts by Jeff Gentry

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Comment: C: Supressing welcome to bioconductor message?
... > Is this what you are looking for? > > suppressMessages(library("Biobase")) Seth, Sean ... That's it, thanks. I knew I'd seen that before, but couldn't track it down. Thanks -J ...
written 9.0 years ago by Jeff Gentry3.9k
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Supressing welcome to bioconductor message?
... I could have sworn that I've seen this before, but my google-fu is failing me at the moment. How can I suppress the "Welcome to Bioconductor" message when BioC loads? I'm trying to develop a module for GenePattern which uses (indirectly) Biobase - but GP spits out a stderr.txt file which really se ...
biobase written 9.0 years ago by Jeff Gentry3.9k • updated 9.0 years ago by Sean Davis21k
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Comment: C: regarding web interface to R coding
... > Python has an extremely straighforward interface to R called RPy. > Python is a very good scripting language for CGI. Also, if you're going that route, Django is a good python based web framework which is real easy to pick up & start using. ...
written 9.1 years ago by Jeff Gentry3.9k
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Comment: C: Getting dChip SNP intensity in BioC?
... > Could be what you are looking for. There's some good info in there, thanks! This isn't quite what I'm after right now though, I'm trying to go in the other direction - exporting data from a BioC session into a file to read into dChip & genepattern (their formats are similar for SNP data, ...
written 10.1 years ago by Jeff Gentry3.9k
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Getting dChip SNP intensity in BioC?
... Hi there ... I'm probably just overlooking something obvious, but I didn't see this in the oligo package. I was hoping to be able to generate the signal values for samples in SNP datasets in the same manner as dChip & genepattern do. As an example, the Genepattern .SNP file format each sample ...
snp oligo written 10.1 years ago by Jeff Gentry3.9k • updated 10.1 years ago by Henrik Bengtsson2.4k
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Comment: C: Converting between old and new annotation packages?
... > Well, you can always get a simple map from your IDs to Entrez gene > from your current package, and then use that as input, so you don't > really need to go back to the originals (granted you may want to go > back as things are likely to have changed since the mapping was done). > ...
written 10.3 years ago by Jeff Gentry3.9k
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Answer: A: Converting between old and new annotation packages?
... Hi Marc ... > The slightly longer answer is that the new style of packages are much > more complex than the old ones because they each contain an actual > sqlite database. So you could convert from the new style package "down" > into one of the older style packages by querying the data ...
written 10.3 years ago by Jeff Gentry3.9k
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Converting between old and new annotation packages?
... Hi there ... Is it possible to directly convert an old style annotation package to the new SQLite *.db style packages without rebuilding from scratch? I didn't see anything when poking around and I'm guessing the answer ranges from "no" to "patches welcome" but figured it was worth a query. Thank ...
annotation convert written 10.3 years ago by Jeff Gentry3.9k
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Comment: C: Reading 80 CEL files.
... > I am curious how long it runs and the configuration of the linux cluster. I've run approximately 1400 hgu133plus2 CEL files on a machine w/ 16GB of memory. IIRC it took a few days (its been a while since I've done anything that large). The CPUs (2 of them, although this process is clearly no ...
written 10.9 years ago by Jeff Gentry3.9k
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Comment: C: RdbiPgSQL: slowness in dbWriteTable
... > Hi, Jeff. The fastest way to get data into postgresql is to use some > version of the copy protocol. I do not know what RdbiPgSQL uses for Yup, your method is essentially what I came across yesterday afternoon, with some slight variations. What you outline is a bit better though. This w ...
written 11.1 years ago by Jeff Gentry3.9k

Latest awards to Jeff Gentry

Centurion 9.0 years ago, created 100 posts.

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