User: Fabrice Tourre

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Posts by Fabrice Tourre

<prev • 92 results • page 1 of 10 • next >
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Comment: C: Deseq2 for down stream analysis
... I need this matrix as the input for Gene Set Enrichment Analysis (GSEA, http://www.broadinstitute.org/gsea/) On Sun, Aug 10, 2014 at 9:41 PM, Fabrice Tourre wrote: > Dear Mike, > > Thank you for your reply. I need a matrix for each gene and sample for > gene set enrichment analysis. &g ...
written 4.1 years ago by Fabrice Tourre970
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Comment: C: Deseq2 for down stream analysis
... Dear Mike, Thank you for your reply. I need a matrix for each gene and sample for gene set enrichment analysis. In you example, how will about this situation: [0,0,0] vs [1,2,3] [0,0,0] vs [10,10,10] I have a lot such case genes. On Sun, Aug 10, 2014 at 9:29 PM, Michael Love wrote: > hi Fa ...
written 4.1 years ago by Fabrice Tourre970
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Deseq2 for down stream analysis
... Dear expert, I've been using DESeq for my RNA-Seq differential expression analysis. Now I want to do GSEA. I have got follow expression value. which one should I used for the down stream analysis? rc, rld or vsd? rc <- counts(dds) rld <- rlog(dds) vsd <- varianceStabilizingTransformation( ...
deseq written 4.1 years ago by Fabrice Tourre970 • updated 4.1 years ago by Michael Love19k
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deseq2: convert ensembl ID to gene symbol.
... Dear expert, I am using Deseq2 and Dexseq to analysis my RNA-seq data. I totally follow the vignette in these packages. In the last output, for the function DEXSeqHTML or HTMLReport, I prefer to use gene symbol, not ensembl ID. For example, I prefer Muc2 to ENSMUSG00000095400. It is more human rea ...
dexseq deseq2 written 4.1 years ago by Fabrice Tourre970 • updated 4 weeks ago by hamidreza_moazzeni200
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Is there any package for meta eqtl?
... Dear expert, I knew GGtools can do eqtl search. But I want a package to do meta eqtl. Because I cannot store all the output from the eqtl. I cannot do two eQTL separately, then combined them. Thank you very much in advance. ...
ggtools written 4.5 years ago by Fabrice Tourre970 • updated 4.5 years ago by Vincent J. Carey, Jr.6.2k
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Comment: C: Annotation different expressed exon. results from DESeq
... Alejandro, Thank you. It is from DESeq. I have added GeneSymbol to the last column. Here how should I understand ENSMUSG00000026727:016, ENSMUSG00000026727:004?does it mean there are two exon 016 and 004 in gene ENSMUSG00000026727 are different expressed in tow conditions? id baseMean baseMeanA ...
written 4.6 years ago by Fabrice Tourre970
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Annotation different expressed exon. results from DESeq
... Dear list, When I use DESeq find different expressed exon in tow conditions. e.g, id baseMean baseMeanA baseMeanB 1 ENSMUSG00000079102:009 851.0096 1697.09604 4.9231156 2 ENSMUSG00000026727:016 239.6701 478.35562 0.9846231 3 ENSMUSG00000026727:004 155.8972 311.79442 0.0000000 Ho ...
deseq written 4.6 years ago by Fabrice Tourre970 • updated 4.6 years ago by Alejandro Reyes1.6k
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Comment: C: How to get gene symbol after deseq?
... Great. Thank you. On Fri, Feb 7, 2014 at 6:32 PM, Steve Lianoglou wrote: > Hi, > > Don't forget that you can always query the ensembl biomart directly > from within R using the biomaRt package: > http://bioconductor.org/packages/release/bioc/html/biomaRt.html > > The user's gu ...
written 4.6 years ago by Fabrice Tourre970
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Comment: C: How to get gene symbol after deseq?
... Jim, I see. Thank you very much. On Fri, Feb 7, 2014 at 5:50 PM, James W. MacDonald wrote: > Hi Fabrice, > > I don't know. It might have something to do with that gene being a predicted > gene. Perhaps we don't annotate such things? Or it may have been placed in > Ensembl between n ...
written 4.6 years ago by Fabrice Tourre970
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Comment: C: How to get gene symbol after deseq?
... Jim, Thank you very much. It makes sense to me. One small question, why ENSMUSG00000082538 is given NA. but it is given a symbol Gm14704 on ENSEMBL. http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG0 0000082538;r=X:70403181-70404054;t=ENSMUST00000120300 On Fri, Feb 7, 2014 ...
written 4.6 years ago by Fabrice Tourre970

Latest awards to Fabrice Tourre

Popular Question 4.1 years ago, created a question with more than 1,000 views. For From location to get the SNP rs ID
Popular Question 4.1 years ago, created a question with more than 1,000 views. For deseq2: convert ensembl ID to gene symbol.

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