problems with finding required R packages

[Sjannie Lefevre]

Hi

I recently discovered that when I run the abundance_estimates_to_matrix script, I only get the counts.matrix and not the TMM.matrix. I get the error 

> library(edgeR)

Error in library(edgeR) : there is no package called ‘edgeR’

Execution halted

when I try to run the 

R --vanilla -q < __tmp_runTMM.R 1>&2

command directly from the terminal. 

I can, however, open a terminal for R directly, and when I am in the R terminal, I can load the packages without problems, indicating that they are installed on the machine (I am running on a cluster). I have also tried copying the commands from __tmp_runTMM.R 1>&2, but genes.TMM.fpkm.matrix is still empty.

Has anyone experienced this or have suggestion has to how I proceed? 

Obviously, creating the matrices is only one problem, but I will not be able to use any of the scripts that uses R "internally" unless I solve this.

Thanks in advance.

Sjannie

[Mark Chapman]

Dear Sjanne,

You should be able to do this:

Open R

source("http://bioconductor.org/biocLite.R")

biocLite('edgeR')

biocLite('DESeq')

biocLite('ctc')

biocLite('Biobase')

biocLite('qvalue')

install.packages('gplots')

install.packages('ape')

before proceeding with DE analysis

And this should give you all the packages you need.

Thanks, Mark

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.
To post to this group, send email to trinityrn...@googlegroups.com.
Visit this group at http://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

--

Dr. Mark A. Chapman

M.Ch...@soton.ac.uk

+44 (0)2380 594396

------------------------------------

Centre for Biological Sciences
University of Southampton

Life Sciences Building 85
Highfield Campus
Southampton
SO17 1BJ

[Sjannie Lefevre]

Dear Mark

Well - I still don't understand why it should be necessary to install the packages when they should already be there, somewhere in the system. But, I did what you suggested anyways, which results in a local R folder being created in my home directory, and it seems trinity can find these libraries.

So it seems to be working now.

Thanks for your answer!

Cheers

Sjannie

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.

To post to this group, send email to trinityrn...@googlegroups.com.
Visit this group at http://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

[Tiago Hori]

It is because your packages weren't installed in the place Trinity looks for them. This can happen for an any number of reasons such as installation method, what distro you are using, your privileges and so on.

T.

"Profanity the is the only language all programmers understand" 

Sent from my iPhone, the universal excuse for my poor spelling.

To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.