Median or Quantile normalization for RNAseq ?

[papori]

Hi all,
Can someone explain me in which normaliztion method it is better to use for my data? or, what i should test for figure it?

I have the options of using Median or Quantile normalization.
My data is from RNAseq (illumina hiseq2000).
We used amplification kit because we had low amount of rna.(a lot of noise)

Actually, i already tried both..
In the median normalization i got ~3000 DE genes where in the quantile i got ~300.
How can i know if the 3000 isn't high rate of FDR?
Or, maybe the quantile isn't suitable with my data and that is why it isn't find all the DE genes?
Is there any consensus on which method to use?

Many thanks!

[Simon Anders]

You haven't even told us which method you used for testing for differential expression. How should we then tell you whether your normalization is suitable for it?

[mbblack]

How many samples? How many groups? Number of replicates in each group? DE analytical method/program? Was the normalized data transformed before DE analysis, and if so, how?

It is pretty hard to give a specific answer without some further details of the data set and what you already did with it.