Hello,

I have previously used DESeq2 for RNAseq analysis. I am attempting to do so again for some new analyses, but am having trouble loading in the functions I need. Here is the code I have successfully used before:

##Load DESeq2
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("stringi")
biocLite("MASS")
install.packages("survival")
biocLite("bit")
library("DESeq2")
setwd("C:/Users/megan/Desktop/Computational/KO-RNAseq")

install.packages("rlang")
biocLite("DESeqDataFromMatrix") 
##Read in your data
Counts_bbmap <- read.table("RNAseqResults.txt", header = TRUE, row.names=1)
sampleInfo <- read.csv("ValuesFile.txt")
sampleInfo <- data.frame(sampleInfo)
dds <- DESeqDataSetFromMatrix(countData = Counts_bbmap, colData = sampleInfo, design = ~Genotype)
dds <- DESeq(dds)
resultsNames(dds)

When I get to this step: 

biocLite("DESeqDataFromMatrix"), I get an error stating: 

" The downloaded binary packages are in C:\Users\megan\AppData\Local\Temp\RtmpUDgflJ\downloaded_packages

Warning message: package ‘DESeqDataFromMatrix’ is not available (for R version 3.4.0)"

I tried downloading and running three different versions of R, 3.3.2 / 3.4.0/3.5.1, but no luck. I have also uninstalled and reinstalled RStudio in addition to changing my library path and the permissions in the path. 

Now, I am getting an additional error: 

> biocLite("DESeq2")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.0

  (2017-04-21).

Installing package(s) ‘DESeq2’

trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/DESeq2_1.18.1.zip'

Content type 'application/zip' length 4542389 bytes (4.3 MB)

downloaded 4.3 MB

package ‘DESeq2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\megan\AppData\Local\Temp\RtmpmOkke2\downloaded_packages

Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  : 

  missing value where TRUE/FALSE needed

I think I must have messed something up trying to solve the initial error. I would really appreciate any help as I am a beginner at R and fear I will mess something else up attempting to fix these errors.

Thanks, 

Megan 

You just need to load the package first I think:

library(DESeq2)
dds <- DESeqDataSetFromMatrix(...)

Installation is just for packages, e.g. BiocManager::install("DESeq2")