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Sorry for this silly question. I use rlog trasfrmation and I found many difference from my samples. There is many values are negative.
rld = rlog(dds1) apply(assay(rld),2,summary) Min. 0.6044 0.02705 -3.248 -3.063 -2.740 -2.165 -3.181 -3.004 1st Qu. 2.5560 1.75300 4.208 4.335 4.391 3.567 4.165 4.133 Median 3.2620 2.40200 6.626 6.546 6.387 6.328 6.500 6.496 Mean 4.4300 3.53900 6.201 6.149 6.096 5.746 6.180 6.054 3rd Qu. 6.1900 4.46900 8.467 8.297 8.121 8.383 8.443 8.346 Max. 17.5900 17.51000 17.130 16.410 16.680 16.270 17.620 17.500
Is it normal obtain negative values after trasormation?