Dear Sir/Madam,

The bioinformaticist whom we cooperated with analyzed the Agilent microarray data with LIMMA and Genespring. As what she said, LIMMA should be more stringent than Genespring, so that we can get more genes with Genespring analysis, but in fact we get less genes by Genespring sometimes and sometimes ¼ of the genes are different, even we both use ANOVA and Benjamini & Hochberg for statistic analysis. So my question is:
1 Is this kind of situation reasonable?
2 What' the reason for the different results between LIMMA and Genespring?

Best wihses!

Ming

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