I am trying to run the qpcrImpute function on the nondetects package on R. I have normalised Ct values for 44 different microRNA for 8 patients and 11 controls, in total there are 836 observations. However some values are missing therefore I am trying to impute them. I have managed to create a qPCR class set, however I run into the following error:

library(HTqPCR)
# Read in table; need to be a matrix, so replace "ND" with NAs
in_data = read.table("C:\\Users\\Admin\\Desktop/david2019_TSV.txt", sep = "\t", stringsAsFactors = FALSE,
                 header = TRUE, row.names = 1, na.strings = "ND")
mat = as.matrix(in_data)

# qPCRset needs featureCategory with "OK", ""Undetermined" or "Unreliable" for each entry
feat_cat = as.data.frame(array("OK", dim=dim(mat)), stringsAsFactors = FALSE)

# Use "Undetermined" for entries corresponding to "ND" in dataset
feat_cat[is.na(mat)] = "Undetermined" 
rownames(feat_cat) = rownames(mat)
colnames(feat_cat) = colnames(mat)


# Create new instance of qPCRset; needs featureNames to be added
 raw = new("qPCRset", exprs = mat, featureCategory = feat_cat)
 featureNames(raw) = rownames(mat)

 # qPRCset object now created:
  raw

  #make identical pData(raw)$sample Name and colnames(exprs(raw) 

  pData(raw)$sampleName <- c("patient","patient.1","patient.2","patient.3","patient.4","patient.5","patient.6","patient.7","hc","hc.1","hc.2","hc.3","hc.4","hc.5","hc.6","hc.7","hc.8","hc.9","hc.10")
   pData(raw)$sampleName


   #deal with target genes
    featureType(raw) <- c    ("Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target","Target")

   #EM algorithim
    raw <- qpcrImpute(raw, dj = TRUE, pyfit = NULL, groupVars=c(NULL),
              batch = NULL, tol = 1, 
              iterMax = 100, outform=c("Single"), formula = NULL, 
              linkglm = "logit")


   **~0 + nrep
   <environment: 0x000000001dea6358>
    Error in Name.s2[ind2] <- names(tst$sigma[i]) : 
     replacement has length zero
     In addition: Warning message:
     Partial NA coefficients for 8 probe(s)**

I have attempted to add a value for length for the replacement using the length function in R but have been successful.

> length(raw$feat_cat) <- "40"
    Warning message:
      In length(raw$feat_cat) <- "40" : length of NULL cannot be changed

I was wondering if anyone would be able to help me with this problem.

You need to have replicate samples, defined by one or more grouping variables. Please take a look at the example in the qpcrImpute man page:

     data(sagmb2011)
     tst <- qpcrImpute(sagmb2011, groupVars="sampleType", 
                       outform=c("Single"), batch=NULL, linkglm = c("logit"))

For your data, I believe you would need to do something like the following:

pData(raw)$sampleType <- rep(c("patient", "healthy_control"), c(8,11))

And then in the function call:

raw <- qpcrImpute(raw, dj = TRUE, pyfit = NULL, groupVars="sampleType",
              batch = NULL, tol = 1, 
              iterMax = 100, outform=c("Single"), formula = NULL, 
              linkglm = "logit")

Hope that helps, Matt