Error with DESeqDataSetFromMatrix is not available (for R version 3.4.1)
1
0
Entering edit mode
@alkimistdoc-13844
Last seen 7.3 years ago

Does anyone have a solution to the following error? Thanks in advance!

Warning message:

package ‘DESeqDataSetFromMatrix’ is not available (for R version 3.4.1)

Here's my session info

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] dplyr_0.7.2                data.table_1.10.4          biomaRt_2.33.4            
 [4] DESeq2_1.16.1              SummarizedExperiment_1.6.3 DelayedArray_0.2.7        
 [7] matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.4      
[10] GenomeInfoDb_1.12.2        IRanges_2.10.2             S4Vectors_0.14.3          
[13] BiocGenerics_0.22.0        BiocInstaller_1.26.0      

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'scales' is missing or broken

deseq2 • 2.0k views
ADD COMMENT
0
Entering edit mode
@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…

DESeqDataSetFromMatrix is not a package. There is a package called DESeq2, and its documentation is here: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

ADD COMMENT
0
Entering edit mode

The error message was copied exactly from RStudio which used the word package, not a matrix made from an object (DESeqDataSet). 

The solution ended up being missing packages and this is the specific code that got me a solution:

source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite("DESeq2")
library(DESeq2).

ADD REPLY

Login before adding your answer.

Traffic: 529 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6