User: Jeff Gentry

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Jeff Gentry3.9k
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Posts by Jeff Gentry

<prev • 385 results • page 2 of 39 • next >
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RdbiPgSQL: slowness in dbWriteTable
... Hi there ... In the past I've had some difficulty inserting some larger tables into postgres using dbWriteTable() from RdbiPgSQL, in terms of speed performance but now I've run into some data.frames which are just too large (although they don't seem to be all that large in practical terms). As an ...
rdbipgsql written 12.2 years ago by Jeff Gentry3.9k • updated 12.2 years ago by John Zhang2.9k
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Comment: C: Reading hundrets of .cel files and QC thereof
... > of .CEL files from NCBI GEO. Take a look at GSE2109, which has 1400 samples > on the plus2 array, if I remember correctly. FWIW I made an exprSet using GSE2109. With 16GB of RAM I still was forced to use just.gcrma() as I could not build it the long way (which was fine for my purposes). ...
written 12.8 years ago by Jeff Gentry3.9k
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Comment: C: How to read and normalize hundreds of CEL files?
... On Mon, 18 Dec 2006, James W. MacDonald wrote: > I know someone who just did around 1000 U133 Plus 2 chips using a Linux > box with 16 Gb RAM using justRMA(), so I am betting you can do all 230 > with your comp. The downside of this is you won't be able to do many QC > plots. Actually i ...
written 12.9 years ago by Jeff Gentry3.9k
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Comment: C: RBGL 1.8.1 installation error on linux
... > based on your suggestions i tested now some new settings, i used the gcc > 3.2.3 compiler (g++32 ) to compile the package (unfortunately there is no > 4.0 version available for FC5) and get, on my system with R 2.3 and > RBGL_1.8.1 the same error as before. but interestingly the instal ...
written 13.5 years ago by Jeff Gentry3.9k
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exprSets from SMD data
... Hello ... I'm looking at building exprSets from the .xls type data from Stanford (http://genome-www5.stanford.edu/index.shtml). To date I've not yet managed to successfully do this, and a bit of searching shows that at the very least others have had some difficulty in the past. I'm curious to see ...
process written 13.8 years ago by Jeff Gentry3.9k
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Reading in mas4 files?
... Hello ... I downloaded the data for the Luo 2002 paper (GEDP accession 230) w/ the intent of building an exprSet out of the data. What they provide appears to be the .txt files output from MAS4 (one for each sample). I've been having difficulty in tracking down if there's a mechanism to read thes ...
written 13.9 years ago by Jeff Gentry3.9k
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Comment: C: [marray] Importing SMD files into marray
... On Mon, 9 Jan 2006, Furge, Kyle wrote: > If you are able to read one file at a time, but not as a collection, it may > be that the arrays are from different print runs and the dimensions of the > arrays are not be exactly the same. > > The last time I remember looking at this, the .xl ...
written 13.9 years ago by Jeff Gentry3.9k
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Answer: A: Rgraphviz: adding weight to an edge
... > But how do I do that? Look at the man page for addEdge, there is a mechanism for adding weights on edge creation. BTW, I checked in a fix for this problem, Rgraphviz version 1.9.2. ...
written 13.9 years ago by Jeff Gentry3.9k
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Comment: C: Rgraphviz: adding weight to an edge
... > edgeA$weight["a~b"] <- 10 # here comes the buggy > edgeA$weight["b~c"] <- 20 # one more > If we dont use the weights it works fine. Is this a bug, or I am > doing something stupid? Well, not that this excuses the segfault (it shouldn't happen, I'll look at this) b ...
written 13.9 years ago by Jeff Gentry3.9k
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Answer: A: Rgraphviz: adding weight to an edge
... > I am using R 2.2.0 with latest releases of bioconductor and other > packages (especially Rgraphviz). I am interested in drawing weighted > graphs using Rgraphviz. It works perfectly fine if I change colour > (color option), labels (label option) of the edge. But if I try to add > w ...
written 13.9 years ago by Jeff Gentry3.9k

Latest awards to Jeff Gentry

Popular Question 10.1 years ago, created a question with more than 1,000 views. For RdbiPgSQL: slowness in dbWriteTable
Centurion 10.1 years ago, created 100 posts.

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