Question: DESeq2 analysis with R
0
gravatar for z.ghseminezhad92
8 months ago by
z.ghseminezhad920 wrote:

Hi, I have 19 Salmon.quant sample(9 control,10 cancer)with csv format that merge them with tximport and now want to perform DESeq2 analysis for my merged data to find what transcripts has diffrent expression in cancer and control my sample_key is like this:

NO.       group           sample 
1            control          GSM366.
2            control          GSM366.
3            control          GSM366.
4            cancer          GSM366.
5            cancer          GSM366.

my txi.salmon is like this:

                        abundance.GSM366.csv....    counts.GSM366.csv    lenght.GSM366.csv
transcript1           0                                                   0                                3.25 
transcript2           4.61                                            0.5                               3.85
transcript3            0                                                  0                                3.26
transcript4           10                                                 1                                3.54
....

and these are my R script:

>library(tximport)
>library(readr)
>setwd("G:/Palindrome/salmon_OUT4/")
>SalmonQuantdir<-"G:/Palindrome/salmon_OUT4/Files"
>setwd(SalmonQuantdir)
>files<-list.files(SalmonQuantdir)
>names(files)<-files
>tx2gene<-read.csv("G:/Palindrome/salmon_OUT4/tx2gene.csv")
>txi.salmon <- tximport(files, type="salmon", tx2gene=tx2gene, importer =read.csv, abundanceCol = "TPM")
>Key_file=read.csv("Sample-key.csv")
>library("DESeq2")

but i don't know how to design condition and how to creat countdata and then perform DESeq2. please help me if you know what scripts is appropriate for R?

rna-seq • 250 views
ADD COMMENTlink modified 7 months ago by jared.andrews076.2k • written 8 months ago by z.ghseminezhad920
4
gravatar for jared.andrews07
7 months ago by
jared.andrews076.2k
St. Louis, MO
jared.andrews076.2k wrote:

Reading the DESeq2 vignettes and associated workflow are good places to start. They are quite easy to follow and explain each step in-depth to help you understand not only the how, but the why. Your design would just be design = ~ group.

ADD COMMENTlink written 7 months ago by jared.andrews076.2k
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 2.3.0
Traffic: 1132 users visited in the last hour