Dear all,

I am trying to analyze PCR data (ct-values) obtained from QIAGEN RT2 Profiler PCR Array. As described in the vignette I prepared tab-delimited text files containing information such as featureType, featurePos etc. as well as ct Values. I have 8 Samples, therefore 8 files each one containg 96 features. My files look like this:

1   A01 Endogenous  Acly    21.85524559021

2   A02 Endogenous  Aco1    25.2785320281982

3   A03 Endogenous  Aco2    23.9263896942139

4   A04 Endogenous  Agl 26.1996746063232
...

This is the code I used trying to create a qPCRset object:

library(HTqPCR)

files <- list.files("./", pattern = "*.txt")
col.info <- list(position = 2, type = 3, feature = 4, ct = 5)
raw <- readCtData(files, n.features = 96, format = "plain",
                  header = FALSE, column.info = col.info, n.data = 8)

This code leads to the following error message:

Error in X[, cols] <- apply(data, 2, function(x) as.numeric(as.character(x))) : 
  Replacement has lenght 0
Additional warning:
In .readCtPlain(readfile = readfile, header = header, n.features = n.features,  :
  96 gene names (rows) expected, got 96

I have no idea how to fix this.

Thanks in advance

Maximilian

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] HTqPCR_1.42.0       limma_3.44.3        RColorBrewer_1.1-2  Biobase_2.48.0      BiocGenerics_0.34.0

loaded via a namespace (and not attached):
 [1] gtools_3.8.2          bitops_1.0-6          affy_1.66.0           stats4_4.0.0         
 [5] KernSmooth_2.23-17    gplots_3.0.4          zlibbioc_1.34.0       gdata_2.18.0         
 [9] affyio_1.58.0         preprocessCore_1.50.0 tools_4.0.0           compiler_4.0.0       
[13] BiocManager_1.30.10   caTools_1.18.0