User: Francois Pepin

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Last seen:
6 years, 9 months ago
Joined:
7 years, 8 months ago
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f*************@sequentainc.com

Posts by Francois Pepin

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Comment: C: strange results with edgeR::goodTuring
... Thanks for checking it out. I'll see if I can find the bug or just work around it. I'm not actually using edgeR in this case other than this function. I was only looking for a an existing implementation of the Good-Turing method and found it in edgeR. Fran?ois On Aug 28, 2012, at 3:32 , Gordon K ...
written 6.7 years ago by Francois Pepin80
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strange results with edgeR::goodTuring
... Hi everyone, I'm trying to use the goodTuring function in edgeR to estimate what kind of pseudocounts to use and I'm getting strange results with small number of categories: x<-c(312,14491,16401,65124,129797,323321,366051,368599,405261,604962) y<- goodTuring(x) y $count [1] 312 14491 1 ...
category edger written 6.7 years ago by Francois Pepin80 • updated 6.7 years ago by Gordon Smyth37k
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Answer: A: Summarising Probe Sets for Agilent 4x44 Arrays
... Hi Sam, It depends a lot on how you have designed your custom array. One of the reason for multiple probes in the whole genome 44k arrays is that they have given different results in their test datasets. In that case, summarizing can be counterproductive. > 1. Is summarisation ever a good ide ...
written 7.5 years ago by Francois Pepin80
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Comment: C: problem with IGH genes in org.Hs.egCHRLOC
... On Nov 1, 2011, at 15:08 , Marc Carlson wrote: > Hi Francois, > > The CHRLOC mappings are based on the data from UCSC, but in order to > find a match to "28473", the UCSC knownToLocusLink table that we > download from UCSC every release has to have an entry in it for > "28473". ...
written 7.6 years ago by Francois Pepin80
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problem with IGH genes in org.Hs.egCHRLOC
... Hi everyone, I'm trying to get information about the IGH alleles and i'm getting strange results from org.Hs.eg.db. For example, if we use IGHV1-3 (located at chr14, starting around 106,471,246 on NCBI & Ensembl websites): > library(org.Hs.eg.db) > get("28473",org.Hs.egSYMBOL) [1] "IGHV ...
biomart written 7.6 years ago by Francois Pepin80 • updated 7.6 years ago by Marc Carlson7.2k
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Comment: C: Agi4x44PreProcess package: Error in build.est
... Hi Jon, Have you tried Jeryk's suggestion in making sure that the name match? Right now they're not matching properly. Francois On Oct 9, 2011, at 7:13 , Jon Mohl wrote: > Francois, > > Here is the results... > >> dim(targets) > [1] 3 4 >> dim(tdPROC) > [1] 41093 ...
written 7.6 years ago by Francois Pepin80
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Answer: A: Agi4x44PreProcess package: Error in build.est
... Hi Jon, You would have to give us some more information about your code. The error message indicates that you don't have the same number of samples data (tdPROC: colnames RGlist$G) as you have information about (targets: pData(targets)). What sare the result of: dim(tdPROC) dim(targets) Francois ...
written 7.6 years ago by Francois Pepin80
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Comment: C: DESEQ problem
... Hi Dawei, The error message is pretty clear. You said method=TRUE and it's unhappy with that. A look at the help for that function (?estimateVarianceFunctions) would tell you what arguments are acceptable for the method. Francois On Sep 28, 2011, at 10:12 , Dawei Li wrote: > > Dear Simon: ...
written 7.7 years ago by Francois Pepin80

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