Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
install problem with R/bioconductor sanwen Bioinformatics 17 02-19-2015 05:56 AM
Bioconductor package -GADEM DNASpeaks MGISEQ (FKA Complete Genomics) 1 06-04-2013 07:52 AM
PubMed: HTSanalyzeR: an R/Bioconductor package for integrated network analysis of hig Newsbot! Literature Watch 0 06-01-2011 03:00 AM
Problem with ShortRead (R, Bioconductor) function readIntensities marlei Bioinformatics 1 11-26-2009 11:23 AM
ShortRead: a bioconductor package for input, quality assessment and exploration Chien-Yuan Chen Literature Watch 0 11-09-2009 02:36 PM

Thread Tools
Old 01-18-2013, 08:38 AM   #1
Junior Member
Location: Tartu, Estonia

Join Date: Jan 2013
Posts: 2
Default Problem with Bioconductor ArrayExpressHTS package


I'm trying to make use of ArrayExpressHTS R package, but I hit the wall in the very beginning.

I used this tutorial An Introduction to ArrayExpressHTS.

And this is my code:

# Set up external tools
options('ArrayExpressHTS.fasta_formatter' = '/Applications/Bioinformatics/fastx_toolkit')
options('ArrayExpressHTS.cufflinks' = '/Applications/Bioinformatics/cufflinks')
options('ArrayExpressHTS.samtools' = '/opt/local/bin')
options('ArrayExpressHTS.bwa' = '/Applications/Bioinformatics/bwa')
options('ArrayExpressHTS.mmseq' = '/Applications/Bioinformatics/mmseq')
options('ArrayExpressHTS.bam2hits' = '/Applications/Bioinformatics/mmseq')
options('ArrayExpressHTS.bowtie' = '/opt/local/bin')
options('ArrayExpressHTS.tophat' = '/opt/local/bin')

# Load libraries

# Get data
aehts <- ArrayExpressHTS("E-GEOD-16190")
The problem is that I get some kind of unknown error from ArrayExpressHTS function:
> aehts <- ArrayExpressHTS("E-GEOD-16190", dir = expfolder)
Fri Jan 18 18:20:21 2013 [AEHTS]  Not Found.
Error in ArrayExpressHTS("E-GEOD-16190") :
Worst part is that it does not say what went wrong, just "Error in ArrayExpressHTS ..." and nothing else.
ilya.kuzovkin is offline   Reply With Quote
Old 01-18-2013, 09:13 AM   #2
Junior Member
Location: Tartu, Estonia

Join Date: Jan 2013
Posts: 2

Turned out to be stupid question.
The answer is that I did not specify reference directory.
This works fine:
aehts <- ArrayExpressHTS("E-GEOD-16190", refdir='reference')
ilya.kuzovkin is offline   Reply With Quote

arrayexpresshts, bioconductor, rna seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 12:55 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO