about the relative levels between 2 lineages of interest

[pchiang5]

Hello,

When I run DD = earlyDETest(gamList, knots = c(2,3 ), pairwise = TRUE, global = T ), how do I know if GAP in lineage 1 is higher or lower compared with lineage 2? If I am only interested in the difference between lineages 1 and 2, how to compare these 2 lineages alone?

Thank you.

head(DD, 1)
waldStat df pvalue waldStat_1vs2 df_1vs2 pvalue_1vs2 waldStat_1vs3 df_1vs3
GAP 143.6421 8 0 39.25156 4 6.180775e-08 76.66353 4
pvalue_1vs3 waldStat_1vs4 df_1vs4 pvalue_1vs4 waldStat_2vs3 df_2vs3
GAP 8.881784e-16 58.38188 4 6.344703e-12 100.2394 4
pvalue_2vs3 waldStat_2vs4 df_2vs4 pvalue_2vs4 waldStat_3vs4 df_3vs4
GAP 0 5.84513 4 0.2110164 87.05488 4
pvalue_3vs4 fcMedian
GAP 0 0.7729633

[koenvandenberge]

Hi @pchiang5 ,

I would recommend using visualization to check the direction of the difference using, e.g., plotSmoothers.