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tutorial [2013/03/30 11:00] sotacam |
tutorial [2013/03/30 11:07] sotacam |
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ENSG00000186891 0.8230924 2.736435 -0.7348520 0.9568449 | ENSG00000186891 0.8230924 2.736435 -0.7348520 0.9568449 | ||
ENSG00000078808 372.5016774 483.708484 -1.0066939 0.9787270 | ENSG00000078808 372.5016774 483.708484 -1.0066939 0.9787270 | ||
+ | Please, remember that this is a toy example and only about 5000 genes are considered, so the results may not be trustable. | ||
+ | |||
+ | Unfortunately, the DE plots in NOISeq package cannot be used yet on these DE results. Please, find below how to draw a plot to illustrate the DE results: | ||
+ | > cond1 = log2(rowMeans(mycounts[,grep("Kidney", colnames(mycounts))]) + 1) | ||
+ | > cond2 = log2(rowMeans(mycounts[,grep("Liver", colnames(mycounts))]) + 1) | ||
+ | > plot(cond1, cond2, cex = 0.7, xlab = "Kidney (Average expression in log-scale)", | ||
+ | ylab = "Liver (Average expression in log-scale)", main = "NOISeqBIO on Marioni's data") | ||
+ | > points(cond1[rownames(mydeg)], cond2[rownames(mydeg)], pch = 20, col = "red", cex = 0.5) |