Hey
I have RNASeq results from infection time points, 24hr, 48hr and 72hr that I would like to compare to 2 controls, M (mycelia)
and S (sporangia). See the metadata below. I am interested in pairwise comparisons for each infection time point and control i.e., M vs 24hr, M vs 48hr, M vs 72hr etc but I would also like to know if there is any difference for using M vs S as control. I think in the former I would do the following;
condition = c(rep("M",3), rep("S",3),rep("24hr",3),rep("48hr",3),rep("72hr",3))
dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition)
Trouble is I don't know how to set up the latter, i.e., I think I wold need a 3rd column with control1, control2 and treatment. But I'm not sure.
Please help!!!
sample condition
P5467_101 M
P5467_102 M
P5467_103 M
P5467_104 S
P5467_105 S
P5467_106 S
P5467_107 24hr
P5467_108 24hr
P5467_109 24hr
P5467_110 48hr
P5467_111 48hr
P5467_112 48hr
P5467_113 72hr
P5467_114 72hr
P5467_115 72hr