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lxl623
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@lxl623-16665
Last seen 6.4 years ago
DESeq2 I installed from latest Bionconductor version is still 1.20 version. Actually, the latest version of DESeq2 is >1.4
Pls see below:
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for
help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0
(2018-04-23).
> packageVersion("DESeq2")
[1] ‘1.20.0’
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
…….
Would you please fix it?
please see the link https://bioconductor.riken.jp/packages/3.0/bioc/html/DESeq2.html
In this link, the version of DESeq2 is 1.6.3, however the corresponding Bioconductor is 3.0. Do I need to transfer my bioconductor from 3.7 to 3.0?
Also, pleas see this link https://bioc.ism.ac.jp/packages/2.14/bioc/vignettes/DESeq2/inst/doc/beginner.pdf
This link is a DESeq2 guidance, the author used in this guidance is version 1.4.5
The first link points to a mirror (or rather: archive) of BioC release 3.0 -- with two releases per year, this is now more than three years old.
Note that the current version is really 1.20 (twenty!) and not 1.2.0 and hence a lot newer than 1.4 or 1.6. If you check the PDF from your second link you will see that it is from 2014.
Simply install BioC release 3.7 and DESeq2 1.20.0 and you'll have the latest version.
My recommendation is to use the latest version of R:
https://cloud.r-project.org/
Then follow the instructions here:
http://bioconductor.org/install
This will give you the latest version of R/Bioc/DESeq2
To access the correct software guide for the software that you have on your machine, you should just run this in R:
vignette("DESeq2")Otherwise, you may end up reading an out-of-date or otherwise incorrect piece of documentation from some random website.