I have 454 results. I have list of contigs and number of reads for each time point. I need to normalized it. My aim is to look for expression.
I am trying to use edgeR. (I am a bit new to this....)
I thought of using calcNormFactor and to use as reference median of all the data or something like this. But I am not sure this is the right way to do it.
Does anyone did it before?
After I got the factor for normalized what do I do with it?
There has recently been some discussion on the BioConductor mailing list here with respect to edgeR
In particular the following paper was highlighted with regards to normalisation and scaling of NGS data. You might want to take a look at it:
"The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of choice for interrogating steady state RNA. In order to discover biologically important changes in expression, we show that normalization continues to be an essential step in the analysis. We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets."