Hello!!
I was wondering if more experienced eyes could help me understand why I am getting an error with the line:
{
DGEList(counts = C[,c(3:33)],
genes = C[, c('GeneID', 'Length')], group = group)
}
That states:
Error in DGEList(counts = C[, c(3:33)], genes = C[, c("GeneID", "Length")], :
Length of 'group' must equal number of columns in 'counts'
Below is a snippet of my code (I am not including all of it simply because the error is at the beginning).
Where the error occurs, I am trying to section off my data (labeled "C"), which is held in Excel, based on the numbers of columns. I am following what someone I know did, where they only had 22 columns (so the code there would be c(3:22) ) and it worked just fine for them. However, when I tried it, it did not work...
Since another individual did this without problems, I'm just not sure why I'm getting this error.
#edgeR analysis
library(limma)
library(edgeR)
library(readxl)
library(dplyr)
library(GO.db)
#call control, call another treatment
group <- factor(c(rep('HD1', 10), rep('HD2', 10)))
#Here it will not work unless you make C variable first and then do function
#to make DGE
C <- read_excel('R/HD1vsHD2.xlsx')
C <- C%>%
{
DGEList(counts = C[,c(3:33)],
genes = C[, c('GeneID', 'Length')], group = group)
}
design <- model.matrix(~group)
counts_keep <- filterByExpr(C, min.count = 20)
counts_filter <- C[counts_keep, ]
counts_norm <- calcNormFactors(counts_filter)
plotMDS(counts_norm)
counts_filter <- estimateDisp(counts_norm, design)
fit <- glmQLFit(counts_filter,design)
Here is a small snipped of my data:
I would appreciate any advice! And thank you in advance! I am still very new to R.