What is limma saying about my data?
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@michael-watson-iah-c-378
Last seen 9.6 years ago
Hi Briefly, I am using R 2.0.1 and limma 1.8.6. I have a double dye-flip experiment with only four arrays, and my targets and design matrix is so: > targets SlideName File Cy3 Cy5 1 TB_43_97 Untreated Cy3/TB_43_97/results.gpr Untreated H202 2 TB_43_106 Untreated Cy3/TB_43_106/results.gpr Untreated H202 3 TB_43_99 Untreated Cy5/TB_43_99/results.gpr H202 Untreated 4 TB_43_101 Untreated Cy5/TB_43_101/results 750vs630.gpr H202 Untreated > design [1] 1 1 -1 -1 After running: > fit <- lmFit(MA, design) > fit <- eBayes(fit) > topTable(fit, adjust="fdr") I find that EVERY single one of my p-values is 0.9999963, apart from the last 10 or so which are NA (as all the data for those spots is NA). Looking at the top gene, it has values of -1.9, -2.9, 2, 1.5, which when flipped the right way and given to t.test show a significant result (for what it's worth). So, why are all my p-values 0.9999963? Have I done something wrong (it is just after Christmas)? Is my data seriously screwed, or is my limma/R seriously screwed? Has anyone seen this before? Cheers Mick
limma limma • 575 views
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