Hello,

I have 2 groups and each group with 3 replicates. Each sample have 50686 genes with RNAseq read counts for each gene. I performed the following function in R to get the normalisation factors

**y <- calcNormFactors(y, method = "upperquartile")**

**I got the following normalisation factors:**

group lib.size norm.factors

WTHC1 WHC 43297217 0.9400238

WTHC2 WHC 46369347 0.9358194

WTHC3 WHC 63202020 1.0778591

WTLR1 WLR 61800948 1.0177353

WTLR2 WLR 66249762 0.9980893

WTLR3 WLR 59552488 1.0382522

But with "TMM" function I got the following normalisation factors

**y <- calcNormFactors(y, method = "TMM")**

group lib.size norm.factors

WTHC1 WHC 43297217 0.9458131

WTHC2 WHC 46369347 0.9676089

WTHC3 WHC 63202020 1.0909037

WTLR1 WLR 61800948 0.9883493

WTLR2 WLR 66249762 0.9905648

WTLR3 WLR 59552488 1.0230927

I do not know which is the better normalisation factor to use? I'm doing the analysis to find the Differential Expressed genes.

Thanks for the help!