User: Rob Scharpf

gravatar for Rob Scharpf
Rob Scharpf240
Reputation:
240
Status:
Trusted
Location:
Last seen:
7 years ago
Joined:
12 years, 11 months ago
Email:
r*******@jhsph.edu

Posts by Rob Scharpf

<prev • 24 results • page 1 of 3 • next >
0
votes
1
answer
484
views
1
answers
Answer: A: MetaArray - results - how to interpret
... Adrian, You probably want poeRes$poe. 'poe' is short for "probability of expression" and is a transformed matrix of gene expression values (number of genes x number of samples). Interpretation of under and over-expression depends on how the phenotype is defined. According to the poe.mcmc helpfil ...
written 7.0 years ago by Rob Scharpf240
0
votes
2
answers
855
views
2
answers
Answer: A: cause 'memory not mapped' when use oligo
... Jianhong, This could be a corrupt file. try reading the cel headers directly: library(affxparser) file.exists(celfiles) for(i in seq_along(celfiles)) readCelHeader(celfiles[i]) Rob On Sep 25, 2012, at 4:21 PM, "Ou, Jianhong" wrote: > Hi all, > > When I run oligo to analysis the data ...
written 7.1 years ago by Rob Scharpf240
0
votes
1
answer
688
views
1
answers
Answer: A: crlmm Illumina cdfName "human1mv1c" not valid
... Hi Richard, This is a bug. I checked in a fix for release version 1.14.3. Both of the following should evaluate to TRUE crlmm:::isValidCdfName("human1mv1c") crlmm:::isValidCdfName("human1mv1cCrlmm") thanks- Rob On Jul 1, 2012, at 1:36 PM, Richard Thompson wrote: > Hi Everyone, > > ...
written 7.3 years ago by Rob Scharpf240
0
votes
0
answers
582
views
0
answers
Copy number analysis
... Hi Raj, In addition to aroma, there's also copy number estimation in crlmm and a hidden Markov model in VanillaICE that incorporates log R ratios and BAFs. Rob On Mar 17, 2012, at 7:00 AM, bioconductor-request@r-project.org wrote: > You can try aroma.affymetrix. Information specific to SNP 6 ...
snp affy vanillaice written 7.6 years ago by Rob Scharpf240
0
votes
1
answer
395
views
1
answer
Empty RangedData with value columns?
... Hi, Would it be possible to have a column (value) in a RangedData object persist even if it has zero length? For example, RangedData(IRanges(), id=character()) has 0 value columns, though I think it would be nice if the 'id' column could persist. Afterall, it is permissable to have a DataFrame ...
written 7.7 years ago by Rob Scharpf240 • updated 7.7 years ago by Michael Lawrence11k
0
votes
1
answer
525
views
1
answers
Answer: A: Possible bug in SNPchip
... On Nov 16, 2011, at 6:00 AM, bioconductor-request@r-project.org wrote: > Message: 1 > Date: Tue, 15 Nov 2011 13:20:15 +0100 > From: Francesco Mancuso > To: > Subject: [BioC] Possible bug in SNPchip > Message-ID: <4EC258FF.5020205@crg.eu> > Content-Type: text/plain > ...
written 7.9 years ago by Rob Scharpf240
0
votes
1
answer
537
views
1
answers
Comment: C: VanillaICE
... Hi Francesco, The LLR is the log likelihood ratio comparing the called state to the 'normal' state. In the context of identifying regions of homozygosity (ROH) from the diallelic genotype calls, the normal state is NOT a region of homozygosity. The likelihood for the two states is computed from t ...
written 8.0 years ago by Rob Scharpf240
0
votes
0
answers
443
views
0
answers
update of crlmm package in BioC 2.7
... The version of crlmm in the BioC 2.7 release branch was updated. This update addresses the NA's reported for copy number at nonpolymorphic markers on chromosome X. Thanks- Rob ...
crlmm written 8.9 years ago by Rob Scharpf240
0
votes
1
answer
662
views
1
answers
Answer: A: crlmm package and allele-specific CNV with Illumina SNP arrays
... Hi Gabriele, The pdf of the vignette is correctly rendered in crlmm v 1.6.6. Or you can find the file illumina_copynumber.Rnw in crlmm/inst/scripts. The script starts from the *.idat files. Rob On Oct 4, 2010, at 6:00 AM, bioconductor-request@stat.math.ethz.ch wrote: > Message: 1 > Date: S ...
written 9.1 years ago by Rob Scharpf240
0
votes
3
answers
543
views
3
answers
Answer: A: problem to compute copy number with crlmm
... On Nov 12, 2009, at 6:00 AM, bioconductor-request@stat.math.ethz.ch wrote: > Message: 4 > Date: Wed, 11 Nov 2009 14:23:31 +0100 (CET) > From: S?ren Gr?ttrup > Subject: Re: [BioC] problem to compute copy number with crlmm > To: > Message-ID: > > > > Content-T ...
written 9.9 years ago by Rob Scharpf240

Latest awards to Rob Scharpf

Popular Question 7.0 years ago, created a question with more than 1,000 views. For smoothScatter axis limits

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 308 users visited in the last hour