On Tue, Nov 6, 2012 at 12:39 AM, Feng Tian <fengtian@bu.edu> wrote:

> Dear all,
> I have some basic questions about two-color array.
> For two-color array with common reference method, one color is for
> interested sample and the other is for common reference. Generally, the
> output is the ratio between interested sample and common reference sample
> after a Lowess method.
> 1) Can I simply regard these ratios as gene expression values (used in
> one-color array) and directly use them to do some analysis since a common
> reference is used?


Yes the log ratios can generally be treated the same as values from single
channel arrays.


> Or I have to calculate the expression value of
> interested sample from raw data (onlyl use one channel)?
> 2) Should I do some inter-chip normalization such as Quantile method used
> in one-colar array?
>

Yes, normalizing the log ratios is usually necessary. Check manufacturers
guidelines / previously published papers using the same platform to find
out what method is most suitable, but quantiles is probably fine.


> 3) Should I check the batch effect? Is there popular or standard method to
> check and alleviate bache effect?
>

You could probably check for batch effect using PCA or a similar clustering
algorithm. Limma implements functionality to correct for batch effect (if
there is evidence of this).

Paul.


> Thank you very much.
>
> Feng Tian
>
> Boston University
>
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-- 
Dr. Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com

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