Supporting files:

Objective: To review transcriptional responses to influenza virus infection using mRNA-seq. The looked at lineage-/MHCII+/CD11b-/CD11c+ cDC sorted from dLN of WT and Ifnlr-/- mice on day 4 following IAV infection, corresponding to the time point of DC accumulation from the lung to the dLN to prime the CD8+ T cell response.

## Loading required package: limma

We will use the limma bioconductor package to perform linear modeling.

source("http://bioconductor.org/biocLite.R")
## Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
## A new version of Bioconductor is available after installing the most
##   recent version of R; see http://bioconductor.org/install
# load limma package
library(limma)
library(stringi)


counts <- read.csv(file="//Users//greener//Downloads//counts.csv",row.names = 1, header=T)

targets <- read.csv(file="//Users//greener//Downloads//targets.csv", header=T)


dim(counts)
## [1] 24060    19
dim(targets)
## [1] 19  6
means <- rowMeans(counts)

filter <- rowSums(counts) >= 75


table(filter)
## filter
## FALSE  TRUE 
## 10804 13256
counts <- counts[filter,]


dim(counts)
## [1] 13256    19

Plot data with log2 tranformation.

boxplot(log2(counts+1), las=2)