User: Davis, Wade

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Davis, Wade350
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Posts by Davis, Wade

<prev • 33 results • page 2 of 4 • next >
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RIPSeeker multicore option not working fully?
... I just wanted to report that, as expected, the suggestion of using options(mc.cores=) to increase the number of cores did work on Linux. Wade -----Original Message----- From: Yue Li [mailto:yueli@cs.toronto.edu] Sent: Wednesday, July 31, 2013 3:59 PM To: Dan Tenenbaum Cc: Davis, Wade; bioconductor ...
go biomart ripseeker written 5.8 years ago by Davis, Wade350
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RIPSeeker multicore option not working fully?
... Dear Yue, I am using your RIPSeeker package and trying to use the option multicore=TRUE. Trying it on both windows and Linux machines, I did not observe multiple cores being used until I first called library(parallel) before running the code below. Also, it appears that only 2 cores were being used ...
annotation go ripseeker written 5.8 years ago by Davis, Wade350 • updated 5.8 years ago by Dan Tenenbaum8.2k
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bug (?) in selectHKgenes() related to geomMean() in SLqPCR package (with fix)
... Dear Dr. Kohl: First, thank you for your work on the SLqPCR package. I've found it very useful over the years. For me, one of the most useful functions in SLqPCR is selectHKgenes(). Recently when calling selectHKgenes(), I came across an error that occurs when NA values are found in the relData mat ...
slqpcr written 6.0 years ago by Davis, Wade350
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glmFit options in edgeR not passed to mglmLS?
... Dear Gordon and Davis, I tried passing maxit to mglmLS when using glmFit via the following code, and I get this message: >fit.filt.tgw <- glmFit(y=dge.filt.tgw, design=rip.design,maxit = 100) Error in glmFit(y = dge.filt.tgw, design = rip.design, maxit = 100) : unused arg ...
written 6.9 years ago by Davis, Wade350 • updated 6.9 years ago by Gordon Smyth37k
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Answer: A: Rsubread package usage and speed questions
... In case others run into the same issue, here is an update: Wei suggested that it was due to a slow I/O issue in my virtual machine, and sure enough that was the issue. More precisely, I was accessing the data from a shared folder. On a native Linux installation, the same code below ran in about 50 ...
written 7.0 years ago by Davis, Wade350
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Rsubread package usage and speed questions
... Dear Wei Shi, I've just started using Rsubread, and I had a few questions. I've got a FASTQ file with about 6.3M reads. I built my reference index (mm10). extdataDir<-"/mnt/hgfs/Z/" setwd(extdataDir) buildindex(basename="mm10_rsubread_index",reference="mm10.fa",memory=1 0000) I then aligned us ...
alignment rsubread written 7.0 years ago by Davis, Wade350
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Answer: A: Definition of probes in lumiHumanAll annotation database
... Javier, When you say definition of the probes, do you just mean the sequence of the probes and/or which probes make up a "gene"? Illumina BeadChip arrays consist of only 1 probe when looking at probe-level data. If you are dealing with gene-summarized data (from the old BeadStudio or GenomeStudio), ...
written 7.1 years ago by Davis, Wade350
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Answer: A: How to combine different annotation (chromosomic, genic) when using easyRNASeq (
... Hi Nico, Thanks for adding these convenient features to easyRNASeq. Everything works fine now. I'm sure other users will benefit from the detailed example below. Thanks again, Wade -----Original Message----- From: Nicolas Delhomme [mailto:delhomme@embl.de] Sent: Friday, March 09, 2012 7:28 AM To: ...
written 7.2 years ago by Davis, Wade350
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Answer: A: Heatmap.2 Trace Line Thickness
... Michael, Heatmap.2 is my favorite heat map function because of its flexibility and options, but I've learned that if you really want to customize things with (any) heat map, you have to edit the code at some point. Look at the code of heatmap.2 by typing heatmap.2. Copy and paste that into an edito ...
written 7.4 years ago by Davis, Wade350
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Answer: A: PFAM gene enrichment test using GOstats and Category
... Henrik, For years I've been using a general function I've to test for GO terms, PFAM, PATH etc but didn't employ the KEGGframe class directly like you do below. Maybe this code snippet from that function will help? What is in each variable should be obvious from the name, I hope. This is the call ...
written 7.4 years ago by Davis, Wade350

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