Good afternoon,
I am analyzing RNAseq data from 2 different populations exposed to 2 experimental treatments and my experimental design is very similar to case study 4.5 in the June 2014 edgeR user guide. Im hoping someone can annotate/explain this part of the R script that deals with model design. Im unsure to what the 1,4 and 5,5 refer and the meaning of ref="mock."
Thanks in advance for help with this admittedly beginner question.
From the user guide:
I am analyzing RNAseq data from 2 different populations exposed to 2 experimental treatments and my experimental design is very similar to case study 4.5 in the June 2014 edgeR user guide. Im hoping someone can annotate/explain this part of the R script that deals with model design. Im unsure to what the 1,4 and 5,5 refer and the meaning of ref="mock."
Thanks in advance for help with this admittedly beginner question.
From the user guide:
Code:
> library(NBPSeq) > library(edgeR) > data(arab) > head(arab) mock1 mock2 mock3 hrcc1 hrcc2 hrcc3 AT1G01010 35 77 40 46 64 60 AT1G01020 43 45 32 43 39 49 AT1G01030 16 24 26 27 35 20 AT1G01040 72 43 64 66 25 90 AT1G01050 49 78 90 67 45 60 AT1G01060 0 15 2 0 21 8 #There are two experimental factors, treatment (hrcc vs mock) and the time that each replicate was conducted: > Treat <- factor(substring(colnames(arab),1,4)) > Treat <- relevel(Treat, ref="mock") > Time <- factor(substring(colnames(arab),5,5))
Comment