The function obtains lower limit of detection as in proteomic analysis.
Examples
suppressMessages(library(Biobase))
data(sample.ExpressionSet, package="Biobase")
exampleSet <- sample.ExpressionSet
Biobase::fData(exampleSet)
#> data frame with 0 columns and 500 rows
Biobase::fData(exampleSet)$lod.max <-
apply(Biobase::exprs(exampleSet),1,quantile,runif(nrow(exampleSet)))
lod <- get.prop.below.LLOD(exampleSet)
x <- dplyr::arrange(fData(lod),desc(pc.belowLOD.new))
knitr::kable(head(lod))
#>
#>
#> | | AFFX.MurIL2_at| AFFX.MurIL10_at| AFFX.MurIL4_at| AFFX.MurFAS_at| AFFX.BioB.5_at| AFFX.BioB.M_at|sex |type | score|
#> |:--|--------------:|---------------:|--------------:|--------------:|--------------:|--------------:|:------|:-------|-----:|
#> |A | 192.7420| 97.13700| 45.81920| 22.54450| 96.7875| 89.0730|Female |Control | 0.75|
#> |B | 85.7533| 126.19600| 8.83135| 3.60093| 30.4380| 25.8461|Male |Case | 0.40|
#> |C | 176.7570| 77.92160| 33.06320| 14.68830| 46.1271| 57.2033|Male |Control | 0.73|
#> |D | 135.5750| 93.37130| 28.70720| 12.33970| 70.9319| 69.9766|Male |Case | 0.42|
#> |E | 64.4939| 24.39860| 5.94492| 36.86630| 56.1744| 49.5822|Female |Case | 0.93|
#> |F | 76.3569| 85.50880| 28.29250| 11.25680| 42.6756| 26.1262|Male |Control | 0.22|
#> |G | 160.5050| 98.90860| 30.96940| 23.00340| 86.5156| 75.0083|Male |Case | 0.96|
#> |H | 65.9631| 81.69320| 14.79230| 16.21340| 30.7927| 42.3352|Male |Case | 0.79|
#> |I | 56.9039| 97.80150| 14.23990| 12.03750| 19.7183| 41.1207|Female |Case | 0.37|
#> |J | 135.6080| 90.48380| 34.48740| 4.54978| 46.3520| 91.5307|Male |Control | 0.63|
#> |K | 63.4432| 70.57330| 20.35210| 8.51782| 39.1326| 39.9136|Male |Case | 0.26|
#> |L | 78.2126| 94.54180| 14.15540| 27.28520| 41.7698| 49.8397|Female |Control | 0.36|
#> |M | 83.0943| 75.34550| 20.62510| 10.16160| 80.2197| 63.4794|Male |Case | 0.41|
#> |N | 89.3372| 68.58270| 15.92310| 20.24880| 36.4903| 24.7007|Male |Case | 0.80|
#> |O | 91.0615| 87.40500| 20.15790| 15.78490| 36.4021| 47.4641|Female |Case | 0.10|
#> |P | 95.9377| 84.45810| 27.81390| 14.32760| 35.3054| 47.3578|Female |Control | 0.41|
#> |Q | 179.8450| 87.68060| 32.79110| 15.94880| 58.6239| 58.1331|Female |Case | 0.16|
#> |R | 152.4670| 108.03200| 33.52920| 14.67530| 114.0620| 104.1220|Male |Control | 0.72|
#> |S | 180.8340| 134.26300| 19.81720| -7.91911| 93.4402| 115.8310|Male |Case | 0.17|
#> |T | 85.4146| 91.40310| 20.41900| 12.88750| 22.5168| 58.1224|Female |Case | 0.74|
#> |U | 157.9890| -8.68811| 26.87200| 11.91860| 48.6462| 73.4221|Male |Control | 0.35|
#> |V | 146.8000| 85.02120| 31.14880| 12.83240| 90.2215| 64.6066|Female |Control | 0.77|
#> |W | 93.8829| 79.29980| 22.34200| 11.13900| 42.0053| 40.3068|Male |Control | 0.27|
#> |X | 103.8550| 71.65520| 19.01350| 7.55564| 57.5738| 41.8209|Male |Control | 0.98|
#> |Y | 64.4340| 64.23690| 12.16860| 19.98490| 44.8216| 46.1087|Female |Case | 0.94|
#> |Z | 175.6150| 78.70680| 17.37800| 8.96849| 61.7044| 49.4122|Female |Case | 0.32|
plot(x[,2], main="Random quantile cut off", ylab="<lod%")
