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!
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!
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