User: gilles.charpigny

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Posts by gilles.charpigny

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Multiple comparisons with Deseq2
... I use deseq2 to compare the transcriptomic signatures of 3 cell types composing the same tissue (A, B, C). The object "res" returns only the comparaison between two cell types? How to obtain other comparisons and in particular the multiple comparison A type vs B type vs C type? *dds <- DESeqD ...
deseq2 written 5 weeks ago by gilles.charpigny0 • updated 5 weeks ago by Michael Love22k
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Comment: C: tximport allfile.exists(files)--> FALSE
... Thank you vry much. I updated R to R3.5. with the latest release of  Bioc and it's ok; I have now difficulties with tximport with Bovine database. I added another question on the forum. ...
written 8 months ago by gilles.charpigny0
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tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
... I used Salmon to  quantify my RNA-seq. As proposed in the Salmon tutorial I downloaded and indexed a bovine transcriptome from Ensembl (ftp.ensembl.org/pub/release-93/fasta/bos_taurus/cdna/Bos_taurus.UMD3.1.cdna.all.fa.gz) After quantification, i plan to use tximport package to aggregate transcrits ...
bos taurus ensembldb tximport tx2gene written 8 months ago by gilles.charpigny0 • updated 8 months ago by James W. MacDonald49k
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Comment: C: tximport allfile.exists(files)--> FALSE
... what i get > data.frame(thefiles = files, doihave = file.exists(files)) thefiles doihave sample1 F:/Documents/R/win-library/3.4/tximportData/extdata/salmon/ERR188297/quant.sf.gz FALSE sample2 F:/Docum ...
written 8 months ago by gilles.charpigny0
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Comment: C: tximport allfile.exists(files)--> FALSE
... I removed tximport/tximportData and reloaded. The erreu code remains the same. Below is a copy of the output. I added a line to see the object file as requested. (The version is R3.4.4) > library(tximportData) > dir <- system.file("extdata", package ="tximportData") > list.files(dir) ...
written 8 months ago by gilles.charpigny0
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tximport allfile.exists(files)--> FALSE
... Using "tximport package" I get the same error message reported 22 months ago by "ctl" but i am not able to resolve the problem with the Michael's answer. When I specify all(file.exists(files)), I get FALSE. I even get this message with the tutorial command lines: library(tximportData) dir <- s ...
tximport written 8 months ago by gilles.charpigny0 • updated 8 months ago by James W. MacDonald49k

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