[BioC] One-color spotted microarrays analysis

[Wolfgang Huber]

Hi Pier-Luc

here's one more option: the "strata" parameter of vsn2 (in the vsn 
package) allows fitting the normalisation model separately for 
(print-tip) groups of probes, for an arbitrary number of one-colour arrays.

If non-linear regression is desired, the method described in [1] is less 
ad hoc and less clumsy than loess against a "virtual second channel".

[1] Normalization and analysis of DNA microarray data by 
self-consistency and local regression, TB Kepler, L Crosby, KT Morgan - 
Genome Biol, 2002.

  Best wishes
	Wolfgang

Naomi Altman ha scritto:
> I am aware of 2 methods.
> 
> You could do quantile normalization.  This is very stringent as it 
> forces the overall expression distribution to be the same on every array.
> 
> You could pick one array (or the genewise mean or median of all arrays) 
> to act as the "control" and lowess normalize everything relative to that 
> array.
> 
> --Naomi
> 
> At 09:05 PM 5/21/2009, Mark Cowley wrote:
>> Hi Pier-Luc,
>> What sort of within array normalisation are you trying to perform? ie
>> what issues have you spotted in your data that you think need removing?
>>
>> There are no print-tip's as such on an agilent array since they're
>> printed by fancy ink jet printers.
>> You can't do lowess, unless you make a 'virtual' 2nd channel, perhaps
>> by taking the average of all channels.
>>
>> cheers,
>> Mark
>> -----------------------------------------------------
>> Mark Cowley, PhD
>>
>> Peter Wills Bioinformatics Centre
>> Garvan Institute of Medical Research, Sydney, Australia
>> -----------------------------------------------------
>> On 22/05/2009, at 12:47 AM, Pier-Luc Poulin wrote:
>>
>>> Hi Massimo and everyone,
>>>
>>> Thanks for the suggestion. I've read documentation about
>>> Agi4x44PreProcess
>>> and Affy packages but I still need advice. Agi4x44PreProcess
>>> contains no
>>> method for normalization between print tips within arrays.
>>>
>>> Our data consists of single color spotted chips. We need to find a way
>>> in bioconductor to do within array normalization. Limma's
>>> normalizeWithinArrays
>>> and marray's maNormMain only do that for two color arrays. I haven't
>>> find
>>> any function for normalizing single channel arrays, except for
>>> affymetrix chips.
>>>
>>> Thanks
>>>
>>> P-L Poulin
>>> Research assistant
>>> Université Laval
>>> www.arborea.ca
>>>
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>>
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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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-- 

Best wishes
      Wolfgang

------------------------------------------------
Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber