[BioC] One-color spotted microarrays analysis

[Pier-Luc Poulin]

Thank Naomi and Mark for the suggestions. Quantile normalization
will be used to normalize between arrays but we have a spatial 
problem within arrays.

Our arrays are custom oligo arrays. We have 48 print-tips on
the array and there is an intensity bias from top to bottom 
of the arrays. I would like to normalize the spatial distribution
of intensities between sub-arrays. Can a 2d spatial normalization
be done without creating a "virtual" channel and using only 
one channel?

Which package and function of BioConductor should I use?

Thanks

P-L Poulin
Research assistant
Université Laval
www.arborea.ca

-----Message d'origine-----
De : Naomi Altman [mailto:naomi at stat.psu.edu] 
Envoyé : May 21, 2009 11:19 PM
À : Mark Cowley; Pier-Luc Poulin
Cc : bioconductor at stat.math.ethz.ch
Objet : Re: [BioC] One-color spotted microarrays analysis

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)
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