[BioC] single color microarray analysis

Gordon Smyth smyth at wehi.edu.au
Fri Mar 4 00:15:29 CET 2005

>Date: Thu, 03 Mar 2005 06:27:13 +0000
>From: "zhihua li" <lzhtom at hotmail.com>
>Subject: [BioC] single color microarray analysis
>To: bioconductor at stat.math.ethz.ch
>Hi netters!
>I would like to know if there r any packages in bioconductor that can
>perform single-color
>microarray analysis on the gene level instead of the probe level. That's to
>say, I've had a matrix with each column representing the expression values
>for a list of genes in a given condition and each row represents the
>expression value of a gene across different conditions. I wanna do all the
>analysis like normalization, plotting....etc. I was at a loss what packages
>should I use?  The affy package generally handles probe-level data - they
>require the colomns to be signals for PM and MM probes, not the expression
>level of genes. The limma package provides some tools to analysis my data,
>such as normalizeQuantiles, etc. But limma generally handles two-color
>microarray data, so there's not much can be done with my data. For example,
>limma's plotting functions usually require both Red and Green signal
>levels. I'm a bit surprised to see that there seems no packages to handle
>single-color microarray data on the gene level.

Just a few more comments. As I've already written, I think the 
functionality for single-channel microarray data is there, you just haven't 
dug deep enough. What I think you're expressing surprise at is the fact 
that the functionality is implicit rather than explicit, i.e., it isn't 
advertised. I think the reason for this is that there has, so far, been no 
individual single-channel platform which has become sufficiently widely 
used to provoke dedicated functions or capabilities in Bioconductor 
packages. For example, there are no read functions designed for 
single-channel data because we don't know which platform to cater for. 
Perhaps the Codelink platform will change this.


>  Could anyone help me?
>Thanks a lot!

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