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
Mike,
Thanks for the reply. After reading back through what I had, I think I had some misplaced quotation marks that were causing an issue. Everything seems to be working fine now.
Best,
Megan