DESeq2 errors for RNA-SEQ data analysis in R studio

Question

[KS]

Hi All,

I am getting an error msgs while running DESeq2 Bioconductor in R studio. When I tried without using the gene_ID column and it does work but then I am unable to see which genes are DEGs.

My Input file:

gene_ID t1.control t2.control t3.control t4.sample t5.sample t6.sample

ENSCAFG1 363 358 409 549 243 437

ENSCAFG2 294 246 242 429 211 300

ENSCAFG3 60 96 26 90 16 17

ENSCAFG4 93 81 89 126 64 79

ENSCAFG5 208 108 174 259 159 177

ENSCAFG6 467 394 412 570 311 373

My R code is:

library(DESeq2)

setwd("/file/path/")

countdata=read.table("file5", header = TRUE)

condition <- factor(c(rep("control",3), rep("sample",3)))

condition

timepoints <- factor(c(rep("t1",1), rep("t2",1), rep("t3",1), rep("t4",1), rep("t5",1), rep("t6",1)))

timepoints

sampleTable <- data.frame(condition = as.factor(condition),
                          timepoints = as.factor(timepoints))

sampleTable

rownames(sampleTable) <- colnames(countdata)

#### Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

deseq <- DESeqDataSetFromMatrix(countData = countdata,
                                    colData = sampleTable,
                                    design = ~condition+timepoints)

deseq
deseq <- deseq[ rowSums(counts(deseq)) > 1, ] ### remove rows that have only 0 and 1
d.deseq <- DESeq(deseq)                    
d.deseq

####  Error in DESeqDataSetFromMatrix(countData = countdata, colData = sampleTable,  : 
  ncol(countData) == nrow(colData) is not TRUE

Much appreciate for any help.

[ATpoint]

Move the gene column of the count data to rownames first so the count table only contains the counts as columns.

[KS]

thank you so much. It is working good after your suggestion.