User: James Perkins

gravatar for James Perkins
Reputation:
60
Status:
Trusted
Location:
Spain
Last seen:
3 years, 5 months ago
Joined:
5 years, 9 months ago
Email:
j**********@gmail.com

Posts by James Perkins

<prev • 7 results • page 1 of 1 • next >
0
votes
2
answers
796
views
2
answers
browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
... I would like to be able to save the UCSC genome browser image view generated by the browserView method in rtracklayer without having to manually do it from the browser. Is this possible? I.e.   for the example: session <- browserSession()   browserView(session,               GRangesForUCSCGenom ...
rtracklayer save file ucsc browsegenome image written 4.2 years ago by James Perkins60 • updated 2.3 years ago by maximilianh10
0
votes
1
answer
901
views
1
answers
Answer: A: Opening Data for NormqPCR (readqPCR)
... Hi Camille There are some examples in the vignette for the package. You can see an example file by using: path <- system.file("exData", package = "ReadqPCR") qPCR.example <- file.path(path, "qPCR.example.txt") More details are given in section 3, page 7 of the vignette, of the different co ...
written 5.0 years ago by James Perkins60
0
votes
0
answers
718
views
0
answers
Measuring shifts in intronic expression independently of exons
... Hi Alejandro, When I say "shrunken FCs" I mean the logFC(case/control) returned by the estimate2FoldChanges function When I say "raw fold changes" I'm talking about manually working out the fold change from the raw data. Is what you describe not essentially calculating a shrunken fold change valu ...
go deseq dexseq ggbio written 5.7 years ago by James Perkins60
0
votes
1
answer
740
views
1
answers
Comment: C: Measuring shifts in intronic expression independently of exons
... Hi Wolfgang, Thanks a lot for all your help on this. One final thing I noticed, which may be of value to anyone following this problem: I noticed that when I use the raw FCs instead of the shrunken FCs to make the volcano plot, the pattern is much clearer: http://postimg.org/image/4ri7pgdht/ Plea ...
written 5.7 years ago by James Perkins60
0
votes
1
answer
740
views
1
answers
Answer: A: Measuring shifts in intronic expression independently of exons
... Hi again, Maybe I should rephrase the last part better. We have a fold change for the E001 "exon" i.e. the summed exonic expression we have a fold change for the E002 "exon" i.e. the summed intronic expression However what we are really interested in is the discrepancy between the two, i.e. intro ...
written 5.7 years ago by James Perkins60
0
votes
1
answer
740
views
1
answer
Measuring shifts in intronic expression independently of exons
... Dear Wolfgang, Martin, list Sorry for the delay Thanks for the explanation re: counting per exons vs. counting per gene wrt multiple transcripts. This doesn't effect my "real data" example where I counted reads mapping to all exons and reads mapping to all introns and classed them as two different ...
go deseq dexseq ggbio written 5.7 years ago by James Perkins60
0
votes
1
answer
499
views
1
answers
Comment: C: Measuring shifts in intronic expression independently of exons
... Hi Wolfgang, list Thank you very much for the helpful tip. I did exactly as you suggested, the code is below. I wanted to do it using the pasilla package in order to create an instructive example, and so that you could potentially recreate the analysis, but strangely sometimes the gene read counts ...
written 5.8 years ago by James Perkins60

Latest awards to James Perkins

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: 331 users visited in the last hour