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Question: Error with DESeqDataSetFromMatrix is not available (for R version 3.4.1)
0
gravatar for alkimistdoc
12 weeks ago by
alkimistdoc0 wrote:

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

ADD COMMENTlink modified 12 weeks ago by Wolfgang Huber13k • written 12 weeks ago by alkimistdoc0
0
gravatar for Wolfgang Huber
12 weeks ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

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 COMMENTlink written 12 weeks ago by Wolfgang Huber13k

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 REPLYlink written 12 weeks ago by alkimistdoc0
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