I want to use the contrast option in DESeq2
ddsctrst <- DESeq(ddsctrst)
ddsctrst
class: DESeqDataSet
dim: 133000 8
exptData(0):
assays(3): counts mu cooks
rownames(133000): comp0_c0 comp100000_c0 ... comp99998_c0 comp99999_c0
rowData metadata column names(36): baseMean baseVar ... maxCooks
cooksOutlier
colnames(8): ABC542 ABC4544 ... ABC4552 ABC4553
colData names(2): condition sizeFactor
head(colData(ddsctrst))DataFrame with 6 rows and 2 columns
condition sizeFactor
<factor> <numeric>
ABC4542 tmp1 1.8234436
ABC4544 tmp3 1.0633168
ABC4547 tmp2 0.4302194
ABC4548 tmp1 1.5796472
ABC4549 tmp2 1.2879635
ABC4551 tmp3 0.9606662
resultsNames(ddsctrst)
[1] "Intercept" "condition_tmp2_vs_tmp1" "condition_tmp3_vs_tmp1"
[4] "condition_tmp4_vs_tmp1"
I want to do this step
rstCtrst <- results(ddsctrst, contrast=c("condition","tmp1","tmp3"))
Error in results(ddsctrst, contrast = c("condition", "tmp1", "tmp3")) :
unused argument (contrast = c("condition", "tmp1", "tmp3"))
kindly provide some suggestion
ddsctrst <- DESeq(ddsctrst)
ddsctrst
class: DESeqDataSet
dim: 133000 8
exptData(0):
assays(3): counts mu cooks
rownames(133000): comp0_c0 comp100000_c0 ... comp99998_c0 comp99999_c0
rowData metadata column names(36): baseMean baseVar ... maxCooks
cooksOutlier
colnames(8): ABC542 ABC4544 ... ABC4552 ABC4553
colData names(2): condition sizeFactor
head(colData(ddsctrst))DataFrame with 6 rows and 2 columns
condition sizeFactor
<factor> <numeric>
ABC4542 tmp1 1.8234436
ABC4544 tmp3 1.0633168
ABC4547 tmp2 0.4302194
ABC4548 tmp1 1.5796472
ABC4549 tmp2 1.2879635
ABC4551 tmp3 0.9606662
resultsNames(ddsctrst)
[1] "Intercept" "condition_tmp2_vs_tmp1" "condition_tmp3_vs_tmp1"
[4] "condition_tmp4_vs_tmp1"
I want to do this step
rstCtrst <- results(ddsctrst, contrast=c("condition","tmp1","tmp3"))
Error in results(ddsctrst, contrast = c("condition", "tmp1", "tmp3")) :
unused argument (contrast = c("condition", "tmp1", "tmp3"))
kindly provide some suggestion
Comment