Not a member of Pastebin yet?
Sign Up,
it unlocks many cool features!
- > head(biomarker[,1:5])
- A2 A3 A4 A6 A7
- A2M 12.4071618 12.631601 12.889748 11.842511 11.574134
- ABCB11 0.5151957 6.176788 5.414905 7.134915 1.247590
- ABCC2 6.7244303 6.487794 10.178615 6.384132 6.089462
- ABCC6 6.3977122 5.823627 7.370761 7.397091 6.071587
- ABCF1 9.1609847 9.893258 10.116638 10.225520 10.838486
- ABCG2 7.6841874 7.738293 6.833152 6.888041 6.030032
- >
- > head(immune[,1:5])
- A2 A3 A4 A6 A7
- A2M 10.904748 11.388404 9.910614 11.513439 12.963609
- ABCB11 5.011380 6.359443 7.145992 8.451947 7.722605
- ABCC2 5.040461 6.477014 3.873996 6.409777 9.133971
- ABCC6 7.798441 7.601848 9.948072 11.628533 12.701460
- ABCF1 8.553597 8.615425 11.145903 10.289098 11.444140
- ABCG2 6.224294 5.629375 8.293416 7.979859 8.603793
- >
- > dim(biomarker)
- [1] 719 56
- > dim(immune)
- [1] 719 56
- >
- > f <- function(x,y){
- + test <- t.test(x,y, paired=TRUE)
- + out <- data.frame(stat = test$statistic,
- + df = test$parameter,
- + pval = test$p.value,
- + conl = test$conf.int[1],
- + conh = test$conf.int[2]
- + )
- + return(out)
- + }
- > t=sapply(seq(ncol(t(biomarker))), function(x) f(t(biomarker)[,x], t(immune)[,x]))
- str(t)
- [list output truncated]
- - attr(*, "dim")= int [1:2] 5 719
- - attr(*, "dimnames")=List of 2
- ..$ : chr [1:5] "stat" "df" "pval" "conl" ...
- ..$ : NULL
- >
- > sapply(t, "[[", "pval")
- Error in FUN(X[[i]], ...) : subscript out of bounds
- >
- > pvalueGenes <- sapply(colnames(biomarker),function(i) t.test(biomarker[i, ],immune[i, ], paired = TRUE)$p.value)
- Error in if (stderr < 10 * .Machine$double.eps * abs(mx)) stop("data are essentially constant") :
- missing value where TRUE/FALSE needed
- In addition: Warning messages:
- 1: In mean.default(x) : argument is not numeric or logical: returning NA
- 2: In if (stderr < 10 * .Machine$double.eps * abs(mx)) stop("data are essentially constant") :
- Show Traceback
- Rerun with Debug
- Error in if (stderr < 10 * .Machine$double.eps * abs(mx)) stop("data are essentially constant") :
- missing value where TRUE/FALSE needed
- pvalueGenes <- sapply(colnames(biomarker),
- function(i) t.test(biomarker[i, ],
- immune[i, ], paired = TRUE)$p.value)
- names(pvalueGenes)[ pvalueGenes < 0.05 ]
Add Comment
Please, Sign In to add comment