[BioC] how to normalize by columns

[Gordon K Smyth]

> Date: Thu, 26 May 2005 03:12:41 -0300
> From: diego huck <diegolugro at yahoo.com.ar>
> Subject: [BioC] how to normalize by columns
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <429568D9.1050308 at yahoo.com.ar>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
>
> Hello
>
>   I am a beginner at bioconductor and R. I have a confussion about how
> to do a normalization which consist of obtain the mean of a column, and
> then substract the mean of the column to each value in the column.
>   x1(1)- mean(col x1)	x2(1)- mean(col x2)
>   x1(2)- mean(col x1)	x2(2)- mean(col x2)
>   x1(3)- mean(col x1)	x2(3)- mean(col x2)
> ....................	...................
>   I have the genes in columns and the conditions in rows.

If you were subtracting condition means, then this would be similar to method="median" of the
normalizeWithinArrays() function in the limma package.  However, subtracting genewise means is not
likely to be a useful normalization method for any sort of expression data.

>   I don't want to stabilize the variance.
>   As you can see is a very simple calculation.
>   I am wondering if could use packages like vsn or affy to do that or is
> more easy to write a script.
>   Futhermore, I have a doubt if such simple normalization is
> conceptually correct whith the objetive of eliminate the effect between
> array.

If you don't think it's right, why do it?  Why not do use one of the methods provided with a
proven track record?  If you want suggestions from BioC people, you could start by explaining
exactly what your data is -- microarray, PCR, one channel, two channel, log-expression,
log-ratios??

Gordon

>   I would to know if I have to iterate any numbers of times the process
> o f calculate the mean of each column and substract the mean.
>
> Thank you
>
> diego lugro
> studient
> universidad de buenos aires
> argentina