How install DESeq2, gplots, RColorBrewer in R?

I want to install (DESeq2), it gives me this message. Can you guide me?

Is there any tutorial to train how I use R for drawing heatmap, pathways...? Thanks

 if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> 
> BiocManager::install("DESeq2")
Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.1.0/library
  packages:
    Matrix, mgcv
Old packages: 'isoband'
Update all/some/none? [a/s/n]:

analysis rna-seq

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updated 5.1 years ago by Ram

• written 5.1 years ago by Bioinformatics1 •

Have you already installed the lastest version of Bioconductor? Perhaps, the problem is there.

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written 5.1 years ago by rodolfo.peacewalker •

1 answer

Have you searched at all? There are dozens of tutorials and vignettes that show how to use these packages. You can ignore this warning (by typing "n" then pressing enter), it's just warning you that you have a few old packages that couldn't be updated.

I recommend doing some reading and trying to follow some of the tutorials available. There are many examples of code that you can mostly copy and paste to get a generic analysis and figures, but you should really try to understand the commands you're running and why they are necessary. It can be a frustratingly slow process to start, but it'll benefit your growth as a scientist greatly in the long run.

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written 5.1 years ago by jared.andrews07

Yes, I found the tutorial. thanks. I want to install a bioconductor. Please see this message? Second question, the program can not read my file " alignment". Error in file(file, "rt") : cannot open the connection this file is on my desktop. When I add the address C/ Desktop.... / Alingment.csv. I received another error. Please guide.

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.1.0/library packages: Matrix, mgcv Old packages: 'isoband' Update all/some/none? [a/s/n]: n Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'DESeq2'

library(DESeq2) library(gplots) library(RColorBrewer)

Read the counts from the downloaded data

speqdata <- read.csv("Allingment.txt") Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'Allingment.txt': No such file or directory

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written 5.1 years ago by Bioinformatics1 •

Do not ask a second question in the same thread. Please stick to one topic.

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written 5.1 years ago by Ram

Thanks jared.andrews07!

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written 5.1 years ago by Bioinformatics1 •

Don't add answers unless you're answering the top level question. Use Add Comment or Add Reply instead as appropriate. I've moved your post to a comment this time.

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written 5.1 years ago by Ram