[BioC] single color microarray analysis

Gordon Smyth smyth at wehi.edu.au
Fri Mar 4 02:07:32 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 

I meant, no single-channel platform other than Affymetrix, of course ...


>  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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