Hello, I only have one gene set, not up and down. My code didn't set
downSet = NULL because this will cause bug.
epi_score <- simpleScore(rankData, upSet=epi_gene, knownDirection=FALSE)
epi_score has some NA score, how to explain no score for some samples? Thanks.
> tail(epi_score) TotalScore TotalDispersion GSM764972 NA NA GSM764973 NA NA GSM764974 NA NA GSM764975 NA NA GSM764976 NA NA GSM764977 NA NA
My gene set size is 140 and only 1 not in expression matrix.
Also I have another gene set named
Mes with the same processing method, and get
NA at same samples.
> filter(emt_score2, is.na(Epi) | is.na(Mes)) # A tibble: 79 x 5 Sample Epi Mes `age:ch1` `Sex:ch1` <chr> <dbl> <dbl> <chr> <chr> 1 GSM764899 NA NA 60-88 M 2 GSM764900 NA NA 60-88 M 3 GSM764901 NA NA 60-88 M 4 GSM764902 NA NA 60-88 F 5 GSM764903 NA NA 50-59 M 6 GSM764904 NA NA 60-88 M 7 GSM764905 NA NA 40-49 F 8 GSM764906 NA NA 60-88 M 9 GSM764907 NA NA 50-59 F 10 GSM764908 NA NA 60-88 F # … with 69 more rows