Dear all,

I'm trying to read raw data from TaqMan TLDA cards. The Ct values were
extracted from SDS file with ExpressionSuite software. I tried to adjust the
files according to the example data provided in the package so currently I
have the data file which looks the following and contains 60 samples:

flag    feature    type    position    Ct    sample
Passed    hsa-let-7a-000377    Target    A1    27.456    Sample1
Passed    hsa-miR-10b-002218    Target    A10    30.314    Sample1
Passed    U6 snRNA-001973    Endogenous Control    A11    30.115    Sample1
Passed    U6 snRNA-001973    Endogenous Control    A12    29.226    Sample1
Passed    hsa-miR-15a-000389    Target    A13    30.238    Sample1

the files.txt contains only the name of the file above and header "File".

When trying to read the data I get the following error:
> files <- read.delim("D:/Magdalena/MicroRNA/Results/Pilot/Card
A/HTqPCR_files/files.txt")

> raw <- readCtData(files=files$File,
path='D:/Magdalena/MicroRNA/Results/Pilot/Card A/HTqPCR_files', n.features =
384, header = TRUE, format="SDS", column.info=list(flag=1, feature=2,
type=3, position=4, Ct=5), n.data = 60, samples = sample, na.value = 40)

Warning messages:
1: In FUN(newX[, i], ...) : NAs introduced by coercion
2: In readCtData(files = files$File, path =
"D:/Magdalena/MicroRNA/Results/Pilot/Card A/HTqPCR_files",  :
  Not enough sample names provided; using Sample1, Sample2, ... instead

3: In readCtData(files = files$File, path =
"D:/Magdalena/MicroRNA/Results/Pilot/Card A/HTqPCR_files",  :
  One or more samples contain NAs. Consider replacing these with e.g. Ct=40
now.

I definitely don't have any NAs in my file (also changed any "Undetermined"
to 40), and in the sample column all the samples names are listed. I can't
find the mistake in my code. I would be very grateful for help.

Best wishes,
Magdalena

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

other attached packages:
[1] HTqPCR_1.12.0      limma_3.14.4       RColorBrewer_1.0-5
[4] Biobase_2.18.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] affy_1.36.1           affyio_1.26.0
 [3] BiocInstaller_1.8.3   gdata_2.12.0.1
 [5] gplots_2.11.0         gtools_2.7.1
 [7] preprocessCore_1.20.0 stats4_2.15.2
 [9] tools_2.15.2          zlibbioc_1.4.0

	[[alternative HTML version deleted]]

