[BioC] single color microarray analysis

Gordon Smyth smyth at wehi.edu.au
Thu Mar 3 23:31:52 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

Mmm. Almost all limma package functions will operate on plain matrices, 
when this is at all sensible. This means you can store your data in a 
matrix for which rows are genes and columns are arrays. Then you have 
access to normalization (normalizeBetweenArrays), differential expression 
(lmFit etc) and plotting (plotMA). And some functions from the affy package 
such as plotDensity() will work for you as well. What was it that you 
wanted to do that you couldn't?


>  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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