[BioC] (no subject)

[Paul Boutros]

>Date: Thu, 9 Sep 2004 22:01:22 +1000 (EST)
>From: "Gordon K Smyth" <smyth at wehi.EDU.AU>
>Subject: Re: [BioC] Finding and controlling for dye bias in Limma
>To: "Sean Davis" <sdavis2 at mail.nih.gov>
>Cc: Bioconductor <bioconductor at stat.math.ethz.ch>
>
>> We have several samples hybed on two-color arrays (treated versus
>> untreated).  Half are in dye-swap.  Can we use Limma to estimate the
>> effect of dye-bias?
>
>Yes
>
>>  A design matrix might look something like:
>>
>> Array	Treatment	Dye-bias
>> 1		1		0
>> 2		1		0
>> 3		1		0
>> 4		1		0
>> 5		-1		1
>> 6		-1		1
>> 7		-1		1
>> 8		-1		1
>>
>> The second coefficient would be significant for "dye-biased genes"
>> while the first would be treatment effect while controlling for dye
>> bias?  Do I understand correctly?
>
>No, the Dye-bias column should be all 1's.

If he has half the samples in each dye-swap status, would it be alternating
1's and -1's?

Array	Treatment	Dye-bias
1		1		1
2		1		-1
3		1		1
4		1		-1
5		-1		1
6		-1		-1
7		-1		1
8		-1		-1

>Gordon
>
>> Thanks,
>> Sean