User: Sylvain Foisy

gravatar for Sylvain Foisy
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Posts by Sylvain Foisy

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Answer: A: Devel version of easyRNASeq: using the simpleRNASeq method gives an error
... Hi Nicolas, On Mar 27, 2014, at 10:40 AM, Nicolas Delhomme wrote: >> I realized that my first attempts at DE analysis were using tophat2 alignments unfiltered for badly mapped reads. > > That?s a good idea since easyRNASeq was not paying attention to that previously apart from mention ...
written 5.4 years ago by Sylvain Foisy80
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Devel version of easyRNASeq: using the simpleRNASeq method gives an error
... Hi to all, I am trying to use the R-devel branch for easyRNASeq to get gene counts from filtered BAM files and I get the following error: > exp<-simpleRNASeq(bamFiles = bfl, param = rParam, nnodes = 1, verbose = TRUE) Error in (function (classes, fdef, mtable) : unable to find an inherite ...
easyrnaseq written 5.4 years ago by Sylvain Foisy80 • updated 5.4 years ago by Nicolas Delhomme320
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Comment: C: DESeq2 in R_devel: a bug?
... Hi Michael, Cool ;-) Thanks for the excellent work!! Best regards S On Mar 5, 2014, at 12:34 PM, Michael Love wrote: > Hi Sylvain, > > Thanks for posting this bug. I should be able to commit a simple change today, which fixes this. > > Mike > > > On Wed, Mar 5, 2014 at ...
written 5.5 years ago by Sylvain Foisy80
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DESeq2 in R_devel: a bug?
... Hi, I used DEseq2 v. 1.3 under R-devel because I have many different values for my design (celltype) and it worked ok. I upgraded my libraries this morning (bad,bad,bad?) and now it is not working. Might this be a bug? > exp.data<-read.table("./count_table_by_gene.txt",header=T,row.names=1) ...
deseq2 written 5.5 years ago by Sylvain Foisy80 • updated 5.5 years ago by Michael Love24k
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Comment: C: Using easyRNASeq package: question about BAM/BAI and links to them
... Hi, On 2013-11-26, at 11:55 AM, Nicolas Delhomme wrote: > 1) Is there any possibility that you have circular symlinks, or symlink chains? I?m not sure how gracefully R would do with symlink chains. Nope, I checked for that. > 2) Are there no permission issues on the bam/bai files or a subs ...
written 5.7 years ago by Sylvain Foisy80
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Comment: C: Using easyRNASeq package: question about BAM/BAI and links to them
... Hi Nicolas, On 2013-11-26, at 11:13 AM, Nicolas Delhomme wrote: > Bonsoir Sylvain, > > I have never encountered that situation. I?ve tried to reproduce it but to no avail. Well, that would not be the first time but usually, I am in your position ;-) Ok, here goes: > 1) report your se ...
written 5.7 years ago by Sylvain Foisy80
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Using easyRNASeq package: question about BAM/BAI and links to them
... Hi, I am trying to use easyRNASeq to create count tables for DESeq analysis. I have about a hundred BAM files with their associated indexes, located in my file system and sorted in folders, on for each provider and in each one folder for each tissue. To not use to much space, I created simlinks fro ...
easyrnaseq written 5.7 years ago by Sylvain Foisy80 • updated 5.7 years ago by Sylvain Foisy30
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arrayQualityMetrics: beutifying the outputs
... Hi, I usually use arrayQualityMetrics with less than 20-30 chips and never cared about the outputs until now. I have a 70 Affy chips study and although the graphs are useful, they are not really presentable: most of the axis legend and labels are really squashed, the typeface barely readable... I ...
affy arrayqualitymetrics written 9.3 years ago by Sylvain Foisy80 • updated 9.3 years ago by Audrey Kauffmann110

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Popular Question 5.4 years ago, created a question with more than 1,000 views. For DESeq2 in R_devel: a bug?

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