[BioC] Does factDesign deal with two-color data?

[Dejian Zhao]

Many thanks for your responses.
The package can deal with two-color data according to Robert. I get the 
answer.
Thanks to Denise and Alberto for suggestions.

Alberto Goldoni wrote:
> Hi Dejian,
>
> for this array data i have used RankProd package that is based on the rank
> product method. The usage is different from affy chip and it depends on the
> experimental design. It is designed for two colour arrays too.
> See the vignette.
>
> I guess with this package you can perform the analysis.
>
> Hope this help.
> Best regards.
>
> 2009/6/11 Robert Gentleman <rgentlem at fhcrc.org>
>
>   
>> Hi Dejian,
>>  Yes, it really just requires that you have an ExpressionSet, but please
>> let us
>> know (on list) if any issues arise.
>>
>>  best wishes
>>    Robert
>>
>>
>> Dejian Zhao wrote:
>>     
>>> Hi,
>>> I learned about factDesign package from a scientific  article which
>>> deals with affy data.
>>> The command library(help=factDesign) invokes some information about this
>>> package.
>>> It shows that this package "Suggests:      affy".
>>> Therefore I wonder whether the factDesign package can deal with
>>> two-color data.
>>> Thanks
>>>
>>> Dejian
>>>
>>>
>>> Package:       factDesign
>>> Title:         Factorial designed microarray experiment analysis
>>> Version:       1.20.0
>>> Author:        Denise Scholtens
>>> Description:   This package provides a set of tools for analyzing data
>>> from a factorial designed microarray experiment,
>>>                or any microarray experiment for which a linear model is
>>> appropriate. The functions can be used to
>>>                evaluate tests of contrast of biological interest and
>>> perform single outlier detection.
>>> Imports:       genefilter, stats
>>> _*Suggests:      affy*_
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>     
>> --
>> Robert Gentleman, PhD
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> PO Box 19024
>> Seattle, Washington 98109-1024
>> 206-667-7700
>> rgentlem at fhcrc.org
>>
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>>
>>     
Hi Dejian,
>
> Currently, factDesign is not directly set up to deal with two-color 
> data, although the functions could be adapted easily enough.  I might 
> recommend the limma package.  The user's manual contains several 
> examples of two-color data analysis.
>
> Hope that helps -
> Denise