Question: single color microarray analysis
12.2 years ago by
zhihua li • 120
zhihua li • 120 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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