Problem loading or running DESeq2
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Entering edit mode
brynnhvoy • 0
@brynnhvoy-15007
Last seen 3.6 years ago

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"

deseq could not find function • 2.1k views
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Entering edit mode
@mikelove
Last seen 2 hours ago
United States

The "Error:" means that DESeq2 did not load. You should re-install the missing package (matrixStats), and potentially repeat until you get no error loading DESeq2.

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Entering edit mode

yes, this worked!!!  For some reason there were four functions that had to be installed separately

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