Dear all,

I am using DESeq2 for differential gene expression analysis. But I am not able to understand I should I put sample information and condition for large set of data as I mention below. I am having around 36 sample consists of

• 2 contrasting genotypes: R316, R512
• 3 different davelopment stage : 5week, 7 week , 9 week 
• 4 different tissue: embryo, endosperm, mesocarp, pericarp
• 2 biological replicate for each

Regards

Yogesh

I recommend that you keep this information in a CSV file. You can create one in a text editor or using Excel or the like. Then read into R using the read.csv() function. Check to see that the values make sense with:

sampleInfo <- read.csv("/path/to/your_filename.csv")
head(sampleInfo)
lapply(sampleInfo, summary)
lapply(sampleInfo, table)