I am trying to run DESeq2 but I get the following error message:
could not find function "DESeqDataSetFromMatrix"
I completely removed all versions of R and R studio and resinstalled them. When I use library(DESeq2), I get the following error:
Error: package ‘matrixStats’ required by ‘DelayedArray’ could not be found
DESeq2 does not show up in my session info, so I am wondering if it cannot find the function mentioned above because the package was not successfully loaded?
I am not a programmer, so any help would be appreciated.
OUTPUT of sessionInfo:
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.38.0 GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 BiocInstaller_1.28.0 edgeR_3.20.8 limma_3.34.8
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 Rcpp_0.12.15 lattice_0.20-35 bitops_1.0-6 grid_3.4.3 zlibbioc_1.24.0 XVector_0.18.0 tools_3.4.3 RCurl_1.95-4.10
[10] compiler_3.4.3 GenomeInfoDbData_1.0.0
>
Output from installation and loading DESeq2
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).
Installing package(s) ‘DESeq2’
also installing the dependency ‘GenomicRanges’
There is a binary version available but the source version is later:
binary source needs_compilation
GenomicRanges 1.30.0 1.30.1 TRUE
Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/GenomicRanges_1.30.0.zip'
Content type 'application/zip' length 3223041 bytes (3.1 MB)
downloaded 3.1 MB
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 ‘GenomicRanges’ successfully unpacked and MD5 sums checked
package ‘DESeq2’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\bhjones.UTK\AppData\Local\Temp\RtmpkbkErT\downloaded_packages
installation path not writeable, unable to update packages: MASS, mgcv, rpart
Old packages: 'GenomicRanges'
Update all/some/none? [a/s/n]:
source("https://bioconductor.org/biocLite.R")a
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
GenomicRanges 1.30.0 1.30.1 TRUE
Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/GenomicRanges_1.30.0.zip'
Content type 'application/zip' length 3223041 bytes (3.1 MB)
downloaded 3.1 MB
package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\bhjones.UTK\AppData\Local\Temp\RtmpkbkErT\downloaded_packages
>
> 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 object is masked from ‘package:limma’:
plotMA
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, cbind, colMeans, colnames, colSums, 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
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
Error: package ‘matrixStats’ required by ‘DelayedArray’ could not be found
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biobase_2.38.0 GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0 BiocInstaller_1.28.0 edgeR_3.20.8 limma_3.34.8
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 Rcpp_0.12.15 lattice_0.20-35 bitops_1.0-6 grid_3.4.3 zlibbioc_1.24.0 XVector_0.18.0 tools_3.4.3 RCurl_1.95-4.10
[10] compiler_3.4.3 GenomeInfoDbData_1.0.0
OUTPUT when trying to run DESeq2 using the following code:
> dataset <- DESeqDataSetFromMatrix(geneCounts_clean = geneCounts_clean,
+ colData = colData,
+ design = ~condition)
Error in DESeqDataSetFromMatrix(geneCounts_clean = geneCounts_clean, colData = colData, :
could not find function "DESeqDataSetFromMatrix"
yes, this worked!!! For some reason there were four functions that had to be installed separately