[BioC] AgiMicroRna with single channel Agilent Array

[axel.klenk at actelion.com]

Oh yes, a couple of years/FES versions ago, Agilent introduced that new
file format (called "compact", IIRC) by omitting some of their many 
columns,
including some important ones, and unfortunately they made this new format
the default. You should be able to fix this by changing some FES setting 
rather
than manually renaming your columns...

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
John Lande <john.lande77 at gmail.com>
To:
axel.klenk at actelion.com, bioconductor at stat.math.ethz.ch
Date:
19.07.2011 17:11
Subject:
Re: [BioC] AgiMicroRna with single channel Agilent Array



Indeed you are right,

I was confused by the fact that the package didn accpted my data.

however I found that the Agilent Feature Extraction is different from the 
one used in the package. the software is version 10.7.3.1. do you think 
this could be the problem? I found that I miss some columns in the imput 
file. specifically the "gMeanSignal", but I found "gMedianSignal", so i 
think it will be fine if I just rename it and gBGUsed, for which I cannot 
fine any correspondance?

thank you very much!


On Mon, Jul 18, 2011 at 7:54 AM, <axel.klenk at actelion.com> wrote:
Dear John,

you don't say what made you think so but the opposite is true:
AgiMicroRna will only work with single channel data. We're
using it for exactly that and it is straightforward -- just follow the
vignette...

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland




From:
John Lande <john.lande77 at gmail.com>
To:
<bioconductor at stat.math.ethz.ch>
Date:
17.07.2011 10:33
Subject:
[BioC] AgiMicroRna with single channel Agilent Array
Sent by:
bioconductor-bounces at r-project.org



dear Bioc,

I have a simple problem. I just got some Agilent single channel data for
miRNA to analyse.

I check in BioC repository and found the package AgiMicroRna that seems
fits
my need, however it seems to me that it can only handle 2 channel
experiment.

do you know any way to properly handle the data with this package or any
other?

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