Question

could not find function "DESeqDataSetFromMatrix

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dastjerdi1974 • 0

@dastjerdi1974-16288

Last seen 6.6 years ago

I installed DESeq packages, however when I try to to execute " cds <- DESeqDataSetFromMatrix(counts, colData, design=~group)" it says that " Error in DESeqDataSetFromMatrix(counts, colData, design = ~group) :
could not find function "DESeqDataSetFromMatrix". Could you please say what is the problem.

deseq2 • 9.0k views

ADD COMMENT • link updated 6.6 years ago by Axel Klenk ★ 1.1k • written 6.6 years ago by dastjerdi1974 • 0

score 1 · Answer 1 · 2018-06-27

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Axel Klenk ★ 1.1k

@axel-klenk-3224

Last seen 16 hours ago

UPF, Barcelona, Spain

Dear Dastjerdi,

as you don't show us the complete code you have used, I need to ask:

have you loaded the package before use, e.g.

library("DESeq2")

?library

HTH.

ADD COMMENT • link 6.6 years ago Axel Klenk ★ 1.1k

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I installed the packages. after typing library ( DESeq2) , I see the following messages in the console;

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
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded
In addition: Warning message:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.