Dear list,
dear Heidi,

I performed a high-throughput analysis with the ABS TaqMan Open Array 
qPCR System, format 112- so ending up with 112 genes analysed in 454 
samples(*2, technical replicates). One Run can be performed with up to 3 
chips (the number of chips varies in my Runs) and  I performed 16 Runs 
in total- taking all Runs together with /rbind/ I end  up with one file 
with 101697 rows (so 112*908) including the header (Output.txt)- it is 
sorted as already shown in several examples online:
Sample    Gene    Reps
S1           Gene1    Rep1
S1           Gene1    Rep2
S1           Gene2    Rep1
S1           Gene2    Rep2    ....and so on..


...and having the same format structure (regarding column names and 
column content) as the Open Array example data provided in the package.

When I try to read in the Ct Data as follows, I always get the error 
code shown below:

 > raw2 <- 
readCtData("Output.txt",n.features=112,n.data=908,format="OpenArray",path="./",
+                    column.info=list(flag="ThroughHole.Outlier", 
feature="Assay.Assay.ID", type="Assay.Assay.Type", 
position="ThroughHole.Address", Ct="ThroughHole.Ct"))

Fehler in `$<-.data.frame`(`*tmp*`, "ThroughHole.Outlier", value = 
character(0)) :
   replacement has 0 rows, data has 101696

 > sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8

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

other attached packages:
[1] HTqPCR_1.10.0      limma_3.12.3       RColorBrewer_1.0-5 
Biobase_2.16.0     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
  [1] affy_1.34.0           affyio_1.24.0 BiocInstaller_1.4.9   
gdata_2.12.0          gplots_2.11.0
  [6] gtools_2.7.0          preprocessCore_1.18.0 stats4_2.15.1         
tools_2.15.1          zlibbioc_1.2.0



Since I am far away from being fluent in R, I still don't know what the 
problem is- I tried nearly EVERYTHING  now:

- as I don't get any kind of flags in the Open Array original output, 
the ThroughHole.Outlier column is filled with 'False' but removing, 
changing, setting flag=NULL
doesn't change a thing
-changing to format=plain will give the same error code, even when flag=NULL

I still don't have a clue if my data structure causes the main problem, 
but how to solve this?
I would appreciate ANY help regarding this problem.

Thanks a lot in advance,
Katharina

-- 
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Katharina Michael
MSc Marine Biology

Katharina.Michael@awi.de


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