Hi, I have 187 samples with two factors: (affected and unaffected) and (male and female) for RNA-Seq data analysis. I have run Kallisto and got output file, now I am using DESeq2 package DGE analysis. I have samples with two factors. Please let me know how to improve the script according to the following metadata.
Here is the metadata information:
affected =94 Male =5 Female: 89 Unaffected: 93 Male: 52 Female:41
Here is the script:
names(files) <- paste0("sample", 1:187) txi.kallisto <- tximport(files, type = "kallisto", txOut = TRUE) head(txi.kallisto$counts) sampleTable <- data.frame(condition = factor(rep(c("affected", "unaffected"), each = 94))) rownames(sampleTable) <- colnames(txi.kallisto$counts)