Dear edgeR users,

I am not a statistician nor R programming geek, please forgive me if I ask
stupid question.

I have RNA-seq data for 2 different genotype of trees with different time
points 0hour(control),3hr,24hours,and 48hours. Each time point has two
replicates.  The experiment design like following:

                         Sample harvested after treatment at
Tree H1     Ctrl    3hrs  24hrs  48hrs
Tree H2     Ctrl    3hrs  24hrs  48hrs

Tree L1     Ctrl    3hrs  24hrs  48hrs
Tree L2     Ctrl    3hrs  24hrs  48hrs

I would like to study genes that are differentially expressed (DE)
throughout the time points in these 2 genotype of trees with edgeR. I read
from the edgeR user guide, the suitable DE analysis method for my expriment
is GLM likelihood ratio test.

After read case study in the user guide, I have the RNA-Seq counts in a
file as below in order to input into the edgeR package.

Ref Tags H1_C H2_C H1_3H H2_3H H1_1D H2_1D H1_2D H2_2D L1_C L2_C L1_3H
L2_3H L1_1D L2_1D L1_2D L2_2D
AA212259 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
AB216460 1 0 0 1 2 1 6 2 1 1 1 0 5 1 3 1
AC221873 3 0 1 0 3 0 0 2 1 0 1 0 2 1 2 0
AD235900 3 1 6 0 5 4 4 4 7 2 4 3 3 0 8 0

I used the following commands to input the counts file into edgeR:

rawdata <- read.delim("file.txt", sep="\t", check.name=FALSE,
stringsAsFactor=FALSE)
trees <-
factor(c("HS","HS","HS","HS","HS","HS","HS","HS","LS","LS","LS","LS","LS","LS","LS","LS"))
treat <-
factor(c("C1","C2","3h1","3h2","24h1","24h2","48h1","48h2","C1","C2","3h1","3h2","24h1","24h2","48h1","48h2"))

I'm not good in R programming, thus, having this file input into the edgeR
and assign the factors as well as design-matrix is a challenge. I'm stuck
how to tell the edgeR about my design matrix.

Could you guys kindly help me on this? Have I input my RNA-Seq counts
correctly? Please correct me if there is any mistake I have done in my
edgeR input.

I appreciate very much for your help and time. Have a nice day.

Best regards,
KJ Lim

	[[alternative HTML version deleted]]

