[BioC] single color microarray analysis

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Thu Mar 3 19:02:42 CET 2005

This is simply not true. I almost always work with a matrix of
normalised expressions (row representing probesets and columns
representing the arrays). And I mostly work with Affymetrix data. I have
recently started using LIMMA and found it to be intuitive and easy.

I would consider "normalization" to be part of the pre-processing stage
and not the analysis. I am afraid that once you have done the summary
step (16 probe pairs into a single probeset), you cannot re-normalise
without the CEL files.

It is true that the LIMMA documentations focuses more on two-colour
arrays because they are more difficult to analyse because of the more
complex designs that are possible due to dye assignment issue. 

Having said that, the LIMMA documentations are pretty clear (with many
example) how to analyse the Affymetrix data. 

See Section 9 onwards of the LIMMA User Guide. There is a very simple
example in Section 9.2.

Regards, Adai

On Thu, 2005-03-03 at 06:27 +0000, zhihua li wrote: 
> 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. Could anyone help me?  
> Thanks a lot!
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