I have a set of data that consists of 4 controls samples and 2 affected samples. I am trying to use Deseq2 for some DE but I am running into an issue. I have been successful working with Deseq2 in the past, but I have always had equal data sets. I have pretty much have been following along through the Deseq2 tutorial here. I figured out where my issue is. There is a line that says
library("tximport") library("readr") library("tximportData") dir <- system.file("extdata", package="tximportData") samples <- read.table(file.path(dir,"samples.txt"), header=TRUE) samples$condition <- factor(rep(c("A","B"),each=3)) rownames(samples) <- samples$run samples[,c("pop","center","run","condition")]
The line that is giving me all the issues is
samples$condition <- factor(rep(c("A","B"),each=3))
It is assume that I have two group and each group contains 3 samples. Even when I take away the "each=3", it still just assumes there are two group with 3 samples in each group. What I really have is two groups, group A containing 4 samples and group B containing 2 samples.
Is there a way to fix this? I know people work with uneven datasets all the time so I hope this is an easy fix.