User: Julien Roux

gravatar for Julien Roux
Julien Roux90
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90
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Location:
Switzerland
Last seen:
5 months, 2 weeks ago
Joined:
9 years, 8 months ago
Email:
j**********@unil.ch

Posts by Julien Roux

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Is it possible to get Ensembl gene descriptions with ensembldb?
... Great, thanks for the quick answer! ...
written 5 months ago by Julien Roux90
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Is it possible to get Ensembl gene descriptions with ensembldb?
... Dear ensembldb maintainers, First, thanks a lot for this great resource! I have a question regarding the "gene description" field. It seems to me that it is not accessible from ensembldb, at least I couldn't find it in the available "columns"... For example, for the gene "Cntnap1" I would like to ...
ensembldb written 5 months ago by Julien Roux90 • updated 5 months ago by Johannes Rainer1.0k
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limma: percent of variance explained
... Dear all, I am analyzing an RNA-seq experiment with voom+limma. The design of the experiment had two fixed effect factors that I combined into one vector including all combinations of the levels of the 2 factors (as explained in the limma user guide, section 9.5), and a random effect that I model us ...
genetics limma written 3.5 years ago by Julien Roux90 • updated 3.5 years ago by Gordon Smyth32k
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strange layering in PCA after removeBatchEffect()
... Dear all, After using limma function removeBatchEffect() on RNA-seq data, I observe a strange behavior when I use PCA to visualize my data. Here are some more details: # dge is my DGEList object with RNA-seq count data y <- predFC(dge, prior.count=2) # When I run a PCA on this matrix, I can obse ...
genetics limma written 4.0 years ago by Julien Roux90 • updated 4.0 years ago by Julien Roux10
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voom and RPKM for multi-species RNA-seq analysis
... Dear all, I am analyzing RNA-seq data generated from liver samples in two species, human and chimp, with 4 biological replicates in each species. I have mapped the reads to 1-to-1 orthologous exons, and I'm aiming at detecting DE exons between species. After reading the "voom" paper (http://www.stat ...
genetics deseq written 4.5 years ago by Julien Roux90
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Comment: C: biomaRt archives
... Thanks a lot! Just don't forget the final "/" in the host name ;) > listMarts(host="may2009.archive.ensembl.org/biomart/martservice/") Regards Julien Rhoda Kinsella a ?crit : > Hi Julien, > You can connect to the ensembl.org archive marts by specifying the URL > of the archive version ...
written 8.4 years ago by Julien Roux90
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biomaRt archives
... Dear mailing list, I am willing to use the biomart archives for ensembl 53, but when using the command: > listMarts(archive = TRUE) ... the most recent ensembl release in 51 Is there a reason for that? Thanks for your help Julien PS: I am using R 2.9.1 with bioconductor 2.4 and biomaRt 2.0.0 ...
biomart written 8.4 years ago by Julien Roux90 • updated 8.4 years ago by Rhoda Kinsella660
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Comment: C: gcRMA: problem compute.affinities.local on gngnf1musa
... Thanks Jim for this clear explanation. I will contact the authors of the method to get their comments on using compute.affinities() instead of compute.affinities.local() Regards, Julien James W. MacDonald a ?crit : > Hi Julien, > > Julien Roux wrote: >> Hello list, >> >> ...
written 9.5 years ago by Julien Roux90
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gcRMA: problem compute.affinities.local on gngnf1musa
... Hello list, In *Schuster et al. 2007 (http://genomebiology.com/2007/8/6/R125) a method is presented allowing to correct *MAS5 present/absent calls based on gcRMA transformed PM threshold values. The R script is available in sup data at http://genomebiology.com/content/supplementary/gb-2007-8-6-r125 ...
annotation probe gcrma written 9.5 years ago by Julien Roux90 • updated 9.5 years ago by James W. MacDonald45k
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topGO enrichment using ensembl gene list
... Hello list, I am using the package "topGO" to analyse GO enrichment of gene sets: My genes are ensembl IDs and are not taken from a microarray, so I had to feed "topGOdata" with a gene2GO list. (see http://thread.gmane.org/gmane.science.biology.informatics.conductor/14 627) I construct that list b ...
microarray go topgo written 9.7 years ago by Julien Roux90 • updated 9.7 years ago by James W. MacDonald45k

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Popular Question 11 months ago, created a question with more than 1,000 views. For topGO enrichment using ensembl gene list

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