User: Furge, Kyle

gravatar for Furge, Kyle
Furge, Kyle210
Reputation:
210
Status:
Trusted
Location:
Last seen:
9 years, 2 months ago
Joined:
15 years, 10 months ago
Email:
k*********@vai.org

Posts by Furge, Kyle

<prev • 19 results • page 1 of 2 • next >
0
votes
1
answer
673
views
1
answers
Answer: A: Problem with chromLoc object.
... Thanks for the report and the example. The package maintainer is on summer holiday for the next few days so there may be a delay in his reply. I think you can manually specify the chromosome names using the "chr" argument in the cset2band() function call. The syntax will be a bit confusing because ...
written 9.2 years ago by Furge, Kyle210
0
votes
1
answer
435
views
1
answers
Answer: A: changing gpr files?
... Yes. A similar strategy has worked for me in the past...attached is some old code that may be helpful. The ann.file referenced in the following code is a simple tab delimited file that holds the old identifier in the first column and the new identifier in the second. something like VAI.ID SEQ. ...
written 10.4 years ago by Furge, Kyle210
0
votes
1
answer
961
views
1
answers
Comment: C: a couple of questions on PGSEA package and GSEA
... Sorry, I forgot to copy this to the BioC group.... I agree the choice of reference set can be difficult. Unfortunately I don't think I am qualified to comment on your particular experimental question :-) The choice of reference is driven by the experimental question. However, there is no conceptua ...
written 11.0 years ago by Furge, Kyle210
0
votes
1
answer
961
views
1
answers
Answer: A: a couple of questions on PGSEA package and GSEA
... 1. Yes, the GSEA and PGSEA methods use different calculations to assess gene set enrichment. I am not aware of another implementation of GSEA other than the one available from the GSEA website, but I have not looked in a while. 2. It is really your preference on how to calculate ratios. I typicall ...
written 11.0 years ago by Furge, Kyle210
0
votes
1
answer
509
views
1
answers
Comment: C: PGSEA question
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080225/ 0d2de81b/attachment.pl ...
written 11.6 years ago by Furge, Kyle210
0
votes
1
answer
509
views
1
answers
Answer: A: PGSEA question
... The range option is *supposed* to work as you describe. Unfortunately, there is a bug in the code. We have found the bug and are working to fix it. We should have an updated version placed in the development repository shortly. In the mean time, a quick fix is to run the PGSEA function with the ve ...
written 11.6 years ago by Furge, Kyle210
0
votes
2
answers
425
views
2
answers
Answer: A: build of bioconductor on R 2.6.1 on mac os 10.5
... This may be an issue between a target specific (PPC 64) R binary installed on your machine and the universal binary packages hosted on CRAN/BioC. Installing BioC using the 'type="source"' option (i.e. biocLite(type="source")) may help clear up the issue. If this does work, also use the type="sour ...
written 11.8 years ago by Furge, Kyle210
0
votes
3
answers
591
views
3
answers
Comment: C: Where do I find the golub_Train dataset?
... To add to the last post -- If memory serves, there was a name change between golubEsets 1.0.1 and the more recent versions (1.2.4) The current "Golub_Train" dataset (1.2.4) was named "golubTrain" in 1.0.1 package I think the example will work if either a) get golubEsets 1.2.4 or b) use the old na ...
written 12.7 years ago by Furge, Kyle210
0
votes
3
answers
591
views
3
answers
Answer: A: Where do I find the golub_Train dataset?
... R is case-sensitive. Instead of "golub_Train" try "Golub_Train". -kyle > From: Benjamin Otto > Date: Tue, 19 Dec 2006 15:30:41 +0100 > To: > Subject: [BioC] Where do I find the golub_Train dataset? > > Dear list members, > > Where do I find the "golub_Train" dataset. It ...
written 12.8 years ago by Furge, Kyle210
0
votes
2
answers
641
views
2
answers
Answer: A: Display Chromosome-bands in a plot
... Provided your data is from human, mouse, or rat the idiogram package may be helpful. -kyle > From: Benjamin Otto > Date: Thu, 13 Jul 2006 16:49:33 +0200 > To: 'BioClist' > Subject: [BioC] Display Chromosome-bands in a plot > > Hi, > > is there some existing function whic ...
written 13.2 years ago by Furge, Kyle210

Latest awards to Furge, Kyle

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 306 users visited in the last hour