Question: edgeR input and design matrix help
0
gravatar for KJ Lim
7.5 years ago by
KJ Lim420
Finland
KJ Lim420 wrote:
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,24hrs,and 48hrs. Each time point has two replicates. The experiment design like as below: 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 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 the user guide, I have the RNA-Seq counts in a file like 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 AA216460 1 0 0 1 2 1 6 2 1 1 1 0 5 1 3 1 AA221873 3 0 1 0 3 0 0 2 1 0 1 0 2 1 2 0 AA235900 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 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]]
edger assign • 628 views
ADD COMMENTlink written 7.5 years ago by KJ Lim420
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 220 users visited in the last hour