On Tue, Feb 3, 2009 at 8:03 AM, Naomi Altman <naomi@stat.psu.edu> wrote:

> Did you remove the Agilent controls before looking at the intensity
> distribution?
>
>
And are these some odd array design like tiling arrays?


>
> At 06:01 AM 2/3/2009, Christian Brière wrote:
>
>> Hi!
>>
>> I am new in microarray analysis and in using Bioconductor. I need to
>> analyse expression data from monocolor Agilent microarrays (105K).  To
>> my surprise, for each array (controls as well as treated samples) the
>> distribution of intensity data is bi-modal. Furthermore, it seems that
>> more than 10% of the genes are differentially expressed between controls
>> and treated samples. Therefore, I wonder what is the best method to use
>> in such case for between arrays normalization. I was told that median or
>> quantile normalization was not adequate. Should  Invariant Set or VSN
>> normalization be better, and what are the packages to use for that ?
>> Thanks for your help
>>
>> --
>>
>> Christian Brière
>> UMR CNRS-UPS 5546
>> BP42617 Auzeville
>> F-31326 Castanet-Tolosan (France)
>> tel: +33(0)5 62 19 35 90
>> Fax: +33(0)5 62 19 35 02
>> E-mail: briere@scsv.ups-tlse.fr <mailto:briere@scsv.ups-tlse.fr>
>>
>> http://www.scsv.ups-tlse.fr
>> http://www.gdr2688.ups-tlse.fr <http://www.gdr2688.ups-tlse.fr/index.php>
>> http://www.ifr40.cnrs.fr
>>
>>
>>
>>
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>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
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