[BioC] probe and probeset removal script

Jenny Drnevich drnevich at uiuc.edu
Wed Mar 5 22:27:21 CET 2008

Hi Philip,

Glad to hear the script was useful to you! I'm not sure of the best 
way to reference a script you got from the BioC archives. It was 
originally written by Ariel Chernomoretz, I only modified it 
slightly, so it rightly should be cited to him. I've never used it in 
a publication, but maybe he has. If you're citing by footnotes, then 
it would be easy to just reference the posting earlier in the thread:

I've also copied the BioC list; I'm sure someone there has dealt with 
this issue before and has some suggestions of what to do if you need 
to cite in the (author, date) format. If it was an actual package, 
then it would be easier to cite, but I'm too computer ignorant to 
know how to do that.


At 02:32 PM 3/5/2008, Philip Bronstein wrote:
>Hello Jenny,
>I am a scientist with the USDA-ARS in Ithaca NY. I am currently writing a
>manuscript in which I use Affymetrix-style microarrays to assess the global
>transcriptional changes to iron concentrations in a plant pathogenic
>bacteria (Pseudomonas syringe). The microarray chips we used were made a
>NimbleGen and they not only included oligos to the open reading frames
>called in the bacterial genome but also probes to intergenic regions of the
>chromosome as well as some genes that were found multiple times in the
>genome. I did not want to include these probes/probesets in my final
>analysis so I was searching the web for ideas on how to remove these before
>I analyzed my data. I came across this webpage
>I used the script that you outlined to remove the unwanted probes and
>probeset and it worked wonderfully! I was wondering how you would like me to
>reference this script in my manuscript? Has it been included in any
>In any case, thank you for the script it made this process much easier!
>Philip Bronstein, PhD
>Cornell University
>Plant Science Bldg Rm 334
>Ithaca, NY 14853
>Office (607) 255-7876
>Lab (607) 255-6733

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

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