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Error in DESeqDataSetFromMatrix(countData = as.matrix(count_Table1), colData = sample_table, : ncol(countData) == nrow(colData) is not TRUE
timepoint<-factor(rep(c("8h","24h","48h","72h","96h"),each=37),levels = c("8h","24h","48h","72h","96h"))
sample_table<-data.frame("samples"=colnames(count_Table1),"timepoint"=timepoint,"user.ID"= a)
library(edgeR)
meanlog2CPM<-rowMeans(log2(cpm(count_Table1) + 1))
hist(meanlog2CPM)
dim(count_Table1)
count_Table1<-count_Table1[meanlog2CPM >1,]
dim(count_Table1)
library(DESeq2)
dds<-DESeqDataSetFromMatrix(countData=count_Table1,colData=sample_table,design = ~timepoint)
normcount<-rlog(dds,blind =FALSE)
It looks like the explanation is right there. Can you explain and show us how you are sure the number of columns in the count data is the same number of rows in the coldata?
Also, why are you putting log CPM into DESeq2? You must know that's not valid.
Thank you for the your suggestions and reply. Yes the number of rows and columns are different and i was wondring how to make them same since I'm new in R . Thank you
Again, why are you putting logCPM into DESeq? If you put the wrong input in, your output will be garbage. If you want to know why your row and column names don't match, you are going to have to look at them.