DESeq2 design
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.
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