Question: Uneven Datasets Deseq2 how to fix factor(rep(c("A","B"),each=3))?
0
gravatar for williamsbrian5064
7 months ago by
williamsbrian5064120 wrote:

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.

assembly rna-seq next-gen R • 231 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by williamsbrian5064120
3
gravatar for h.mon
7 months ago by
h.mon21k
Brazil
h.mon21k wrote:
samples$condition <- factor( c( "A","A","A","A","B","B" ) )
ADD COMMENTlink modified 7 months ago • written 7 months ago by h.mon21k

BOOM! Worked like a charm. Thank you very very much for your help.

ADD REPLYlink written 7 months ago by williamsbrian5064120
1

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ADD REPLYlink modified 7 months ago • written 7 months ago by genomax59k
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