I recently completed a 22 day time course with a resistant and susceptible plant with five timepoints (0hr - control), 1dpi, 7dpi, 14dpi, and 22dpi. I was able to do three replicates and sequenced my smaples t get RNAseq libraries (30 libraries total). I now have begun my RNA seq analysis in DESeq2. I have set up my samples object for the comparisons like so:
I am using my treatment column to design my comparisons. I have done the following comparisons so far:
RA-SA
RB-SB
RC-SC
RC-SD
RE-SE
RB-RA
RC-RA
RD-RA
RE-RA
SB-SA
SC-SA
SD-SA
SE-SA
My DESEq2 comparison is done withe the follwing code:
And my results are retrieved like so:
I now want to do the following comparisons:
I am not sure of what code to use. Would anybody be able to point me in the right direction? Any help appreciated.
Code:
sample timepoint treatment genotype S1A_rep1 0 SA S S1A_rep2 0 SA S S1A_rep3 0 SA S S1B_rep1 1 SB S S1B_rep2 1 SB S S1B_rep3 1 SB S S1C_rep1 7 SC S S1C_rep2 7 SC S S1C_rep3 7 SC S S1D_rep1 14 SD S S1D_rep2 14 SD S S1D_rep3 14 SD S S1E_rep1 22 SE S S1E_rep2 22 SE S S1E_rep3 22 SE S R1A_rep1 0 RA R R1A_rep2 0 RA R R1A_rep3 0 RA R R1B_rep1 1 RB R R1B_rep2 1 RB R R1B_rep3 1 RB R R1C_rep1 7 RC R R1C_rep2 7 RC R R1C_rep3 7 RC R R1D_rep1 14 RD R R1D_rep2 14 RD R R1D_rep3 14 RD R R1E_rep1 22 RE R R1E_rep2 22 RE R R1E_rep3 22 RE R
RA-SA
RB-SB
RC-SC
RC-SD
RE-SE
RB-RA
RC-RA
RD-RA
RE-RA
SB-SA
SC-SA
SD-SA
SE-SA
My DESEq2 comparison is done withe the follwing code:
Code:
dds <- DESeqDataSetFromTximport(txi, sample, ~treatment)
Code:
results(deseqData, contrast=c("treatment","RB","RA"))
Code:
(RB - SB) - (RA - SA) (compare RB and SB, then compare that to RA and SA, compared) (RE + SE) - (RA + SA) (RE + RD) - (RC + RB) [(RE + RD) - (RC + RB)] - [(SE + SD) - (SC - SB)] (compare the early vs late response of the R plants to that of the susceptible)
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