Question: How to filter out an RNA-seq differential expression data set?
gravatar for pvaysberg
5.1 years ago by
United States
pvaysberg0 wrote:

Hello, I have a data set with expression values (counts). I assembled the transcriptome myself, since there is no reference to map to. I started with 130,000 transcripts (rows on my data table) and brought it down to about 70,000 by filtering out all transcripts with (sum of row FPKM) < 1. This was to eliminate lowly expressed gene and stochastic noise. I don't know how to futher filter my dataset to only find differentially expressed genes, unfortunately. Any tips or resources? 

statistics rna-seq R • 2.2k views
ADD COMMENTlink modified 5.1 years ago by Devon Ryan91k • written 5.1 years ago by pvaysberg0
gravatar for Devon Ryan
5.1 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

You need to calculate adjusted p-values and filter according to that. With FPKM, people often use an ANOVA or similar linear model.

ADD COMMENTlink written 5.1 years ago by Devon Ryan91k
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