Question

Error in DESeqDataSetFromMatrix

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fnu.chelsea • 0

@947f0210

Last seen 2.5 years ago

Germany

Hi,

I have been trying to run Deseq2 analysis, but I'm unable to use DESeqDataSetFromMatrix function. I get the following error Error in DESeqDataSetFromMatrix(countData = read_Count, colData = reordered_metaData, : could not find function "DESeqDataSetFromMatrix"

Code should be placed in three backticks as shown below


dds <- DESeqDataSetFromMatrix(countData= read_Count,
                              colData = reordered_metaData,
                              design = ~ 1)

sessionInfo( )

DESeq2 • 1.4k views

ADD COMMENT • link 2.5 years ago fnu.chelsea • 0

score 1 · Answer 1 · 2022-06-13

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Basti ▴ 780

@7d45153c

Last seen 1 day ago

France

Did you run library(DESeq2) before ?

ADD COMMENT • link 2.5 years ago Basti ▴ 780

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yes, I did

ADD REPLY • link 2.5 years ago fnu.chelsea • 0

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My library is not being loaded properly. error: genomicrange package is not there.

I'm unable to install this package even after using this:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("GenomicRanges")

ADD REPLY • link 2.5 years ago fnu.chelsea • 0

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What ERROR do you get when doing BiocManager::install("GenomicRanges")? Please include the full output of the commands you are trying so we can better assist you.

ADD REPLY • link 2.5 years ago shepherl 4.1k

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ERROR: 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.2 (2021-11-01) Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'GenomicRanges'

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages: [1] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 BiocGenerics_0.40.0 BiocManager_1.30.18

loaded via a namespace (and not attached): [1] compiler_4.1.2 tools_4.1.2 GenomeInfoDbData_1.2.7 RCurl_1.98-1.7 bitops_1.0-7

ADD REPLY • link 2.5 years ago fnu.chelsea • 0