User: gilles.charpigny

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Posts by gilles.charpigny

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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 3 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 3 months ago by gilles.charpigny0 • updated 3 months ago by James W. MacDonald48k
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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 3 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 3 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 3 months ago by gilles.charpigny0 • updated 3 months ago by James W. MacDonald48k

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