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Old 01-18-2013, 08:38 AM   #1
ilya.kuzovkin
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Location: Tartu, Estonia

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

Hi,

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:

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
library("ArrayExpressHTS")

# Get data
aehts <- ArrayExpressHTS("E-GEOD-16190")
The problem is that I get some kind of unknown error from ArrayExpressHTS function:
Code:
> 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.
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Old 01-18-2013, 09:13 AM   #2
ilya.kuzovkin
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Location: Tartu, Estonia

Join Date: Jan 2013
Posts: 2
Default

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