DESeq2
1
0
Entering edit mode
3 months ago
Rob ▴ 120

Hi people I get error in this code:

rawdata <- read.csv("data.csv",
header = TRUE,row.names = 1, stringsAsFactors = FALSE,
check.names = F) #rawdata is a count matrix

library(Biobase)
library(GenomicRanges)
library(tibble)
library(dplyr)
install.packages("BiocManager")

BiocManager::install("SummarizedExperiment")

se <- SummarizedExperiment(rawdata)
library(DESeq2)
dds <- DESeqDataSet( se, design = ~ 1 )  ##this gives error

error is: renaming the first element in assays to 'counts'
Error in DESeqDataSet(se, design = ~1) :
counts matrix should be numeric, currently it has mode: list

RNA-Seq • 411 views
1
Entering edit mode

The error is already stated clearly:

counts matrix should be numeric, currently it has mode: list


It appears that your first file is not in proper format, but tough to tell for sure without seeing at least several lines from each input file.

I think with each question your goal should be to give us as much information as possible, as that will cut down on time for follow-up questions and answers.

0
Entering edit mode

EDIT: I apologize, the answerer in the other thread asked you explicitly to open a new question, and I did not see that part. I especially apologize for the remark on suspension and take it back.

0
Entering edit mode
3 months ago
ATpoint 60k

Try using a dedicated converter function:

dds <- as(se, "DESeqDataSet")