I have extracted raw count data from raw reads file, and my data set is as follows: The first column is the gene name, and the next four rows are counts for each sample, the first two being control data, and the next two being experimental data of interest. It is very simple, and looks like below. Please note I have already cleaned the data and accounted for feature overlap and intersection.
gene_symbol_1 1 2 3 4
gene_symbol_2 2 3 4 5
gene_symbol_3 0 11 2 7
The parameters for DESeqDataSetFromMatrix() are as such:
countData := can just be the raw counts
but I am confused as to enter the variables colData, and design.
How can encode the colData matrix? After I have properly encoded colData, how do I input design? I have observed the following sources, but it is not so clear in my context, because I do not have a "summarized experiment" object:
Thank you in advance for your help.