Hey Michael

DESeq2 dose not work and I receive this message when I try to run library(DESeq2)

library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
    parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames,
    colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To
    cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply

Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘colorspace’
In addition: Warning messages:
1: package ‘DESeq2’ was built under R version 3.5.2 
2: package ‘matrixStats’ was built under R version 3.5.2

and when I try to run the following script

  data <- read.table("Single.cntTable",header=T,row.names=1)
groups <- factor(c(rep("TGroup",6),rep("CGroup",6)))
min_read <- 1
data <- data[apply(data,1,function(x){max(x)}) > min_read,]
sampleInfo <- data.frame(groups,row.names=colnames(data))
library(DESeq2, quietly=T)
dds <- DESeqDataSetFromMatrix(countData = data, colData = sampleInfo, design = ~ groups)
dds$condition = relevel(dds$groups,"CGroup")
dds <- DESeq(dds)
res <- results(dds,independentFiltering=F)
write.table(res, file="Single_gene_TE_analysis.txt", sep="\t",quote=F)

I receive this output

> data <- read.table("Single.cntTable",header=T,row.names=1)
> groups <- factor(c(rep("TGroup",6),rep("CGroup",6)))
> min_read <- 1
> data <- data[apply(data,1,function(x){max(x)}) > min_read,]
> sampleInfo <- data.frame(groups,row.names=colnames(data))
> library(DESeq2, quietly=T)
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘colorspace’
In addition: Warning message:
package ‘DESeq2’ was built under R version 3.5.2 
> dds <- DESeqDataSetFromMatrix(countData = data, colData = sampleInfo, design = ~ groups)
Error in DESeqDataSetFromMatrix(countData = data, colData = sampleInfo,  : 
  could not find function "DESeqDataSetFromMatrix"
> dds$condition = relevel(dds$groups,"CGroup")
Error in relevel(dds$groups, "CGroup") : object 'dds' not found
> dds <- DESeq(dds)
Error in DESeq(dds) : could not find function "DESeq"
> res <- results(dds,independentFiltering=F)
Error in results(dds, independentFiltering = F) : 
  could not find function "results"
> write.table(res, file="Single_gene_TE_analysis.txt", sep="\t",quote=F)
Error in is.data.frame(x) : object 'res' not found

I wonder if you could help me please

thanks

Sam

Try reinstalling Bioconductor