Hi Experts, i have this feature counts matrix for 23 samples (each containing multiple replicates ranging 3-16). Among these 23 samples some are untreated for some to which i want to compare with or call DESeqDataSet. the samples are something as-
run treatment_concen cell line conditions time SRRxxxx1 0 A1 untreated 24hr SRRxxxx2 2 A1 treated 24hr SRRxxxx3 0 A1 untreated 24hr SRRxxxx4 0.2 A1 treated 24hr SRRxxxx5 0 A1 untreated 24hr SRRxxxx6 15 A1 treated 24hr SRRxxxx7 A1 untreated 9hr SRRxxxx8 A1 treated 9hr SRRxxxx9 0 A1 untreated 24hr SRRxxxx10 2 A1 treated 24hr SRRxxxx11 H1 healthy SRRxxxx12 H1 paitent SRRxxxx13 0 A1 untreated 24hr SRRxxxx14 0.02 A1 treated 24hr SRRxxxx15 0 A1 untreated 24hr SRRxxxx16 2 A1 treated 24hr SRRxxxx17 2 A1 treated 24hr SRRxxxx18 0 N1 untreated 12hr SRRxxxx22 3 N1 treated 12hr SRRxxxx23 0 N1.1 treated 12hr SRRxxxx19 3 N1.1 untreated 12hr SRRxxxx20 N1.1 treated 6hr SRRxxxx21 N1.1 treated 12hr
can you please suggest my design formula for this. basically there is untreated and treated for each group with multiple replicates. any help is much appreciated.
Do you want to compare untreated to treated regardless of time, or taking into account time?
I want to compare respective untreated vs treated, for ex. SRRxxxx13 untreated vs SRRxxxx14 treated. may be i should remove this time point column if that makes these comparisons streamlined for DESeq object. alternatively i was also thinking grouping them in to 1,2,3,4 ... conditions and call DESeq but am not sure if that will give me a comparison result when extracting results using contrast ?