Hi all,

I'm having some issue with using the geNorm method in norm.qPCR to select the best HK genes from a dataset of mine. The error message that is being returned is "Error in R[i] <- Symbols[ind] : replacement has length zero."

My file has 98 plates, each with 380 detectors. Here is a snippet of the organization of the tab delimited txt file

Sample Detector Cq

CAV_Plate_55 ath_miR159a_000338 Undetermined

CAV_Plate_1 ath_miR159a_000338 Undetermined

CAV_Plate_1 hsa_let_7a_000377 Undetermined

CAV_Plate_1 hsa_let_7b_002619 22.531

CAV_Plate_1 hsa_let_7c_000379 30.198

CAV_Plate_1 hsa_let_7d_002283 28.422

CAV_Plate_1 hsa_let_7e_002406 26.968

CAV_Plate_1 hsa_let_7f_000382 36.8

Script below:

library(ReadqPCR) 
library(NormqPCR)
setwd("C:/Users/tonil/Documents/R/win-library/3.4/ReadqPCR/exData")
path <- system.file("exData", package = "ReadqPCR")
normies <- file.path(path, "normalizers.set.2.tab.delim.txt")
normies.batch <- read.qPCR(normies)

options(width = 68)
data(geNorm)
str(exprs(normies.batch))

WHY <- selectHKs(normies.batch, method = "geNorm", Symbols = featureNames(normies.batch), minNrHK = 2, log = FALSE)

from terminal:

> library(ReadqPCR) 
> library(NormqPCR)
> setwd("C:/Users/tonil/Documents/R/win-library/3.4/ReadqPCR/exData")
> path <- system.file("exData", package = "ReadqPCR")
> normies <- file.path(path, "normalizers.set.2.tab.delim.txt")
> normies.batch <- read.qPCR(normies)
There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> options(width = 68)
> data(geNorm)
> str(exprs(normies.batch))
 num [1:380, 1:98] NA NA 22.5 30.2 28.4 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:380] "ath_miR159a_000338" "hsa_let_7a_000377" "hsa_let_7b_002619" "hsa_let_7c_000379" ...
  ..$ : chr [1:98] "CAV_Plate_1" "CAV_Plate_10_" "CAV_Plate_11_" "CAV_Plate_12_" ...
> 
> WHY <- selectHKs(normies.batch, method = "geNorm", Symbols = featureNames(normies.batch), minNrHK = 2, log = FALSE)
Error in R[i] <- Symbols[ind] : replacement has length zero
> 

That's literally all of it and I'm not sure where to go from here. Google searches are not turning up much on this problem for this package.