[BioC] replicating ReadqPCR

[Franklin Johnson [guest]]

Dear James and Matthias,

I am trying to repeat the steps to read in data.
The data is modified from my experiment into a tab-delim file which is identical to qPCR.techReps.txt:
Well 	Plate ID	Sample	Detector	Cq
1	caseA	one	actin_untreated_0d_TechRep.1	20.3
2	caseB	one	actin_triton_1d_TechRep.1	20.91
3	caseB	one	actin_triton_3d_TechRep.1	21.08
4	caseB	one	actin_triton_7d_TechRep.1	21
5	caseB	one	actin_triton_14d_TechRep.1	21.32
6	caseC	one	actin_meja_1d_TechRep.1	21.36
7	caseC	one	actin_meja_3d_TechRep.1	21.22
8	caseC	one	actin_meja_7d_TechRep.1	21.79
9	caseC	one	actin_meja_14d_TechRep.1	22.07
1	caseA	two	actin_untreated_0d_TechRep.2	20.1
2	caseB	two	actin_triton_1d_TechRep.2	21.1
3	caseB	two	actin_triton_3d_TechRep.2	21.12
4	caseB	two	actin_triton_7d_TechRep.2	21.3
5	caseB	two	actin_triton_14d_TechRep.2	21.21
6	caseC	two	actin_meja_1d_TechRep.2	21.5
7	caseC	two	actin_meja_3d_TechRep.1	21.4
8	caseC	two	actin_meja_7d_TechRep.2	22
9	caseC	two	actin_meja_14d_TechRep.2	22.1
10	caseA	one	lox22_untreated_0d_TechRep.1	22.28
11	caseB	one	lox22_triton_1d_TechRep.1	23.65
12	caseB	one	lox22_triton_3d_TechRep.1	24.77
13	caseB	one	lox22_triton_7d_TechRep.1	23.99
14	caseB	one	lox22_triton_14_TechRep.1	24.47
15	caseC	one	lox22_meja_1d.TechRep.1	22.13
16	caseC	one	lox22_meja_3d_TechRep.1	21.99
17	caseC	one	lox22_meja_7d_TechRep.1	24.17
18	caseC	one	lox22_meja_14d_TechRep.1	24.17
10	caseA	two	lox22_untreated_0d_TechRep.2	22.4
11	caseB	two	lox22_triton_1d_TechRep.2	23.84
12	caseB	two	lox22_triton_3d_TechRep.2	24.9
13	caseB	two	lox22_triton_7d_TechRep.2	24.2
14	caseB	two	lox22_triton_14_TechRep.2	24.6
15	caseC	two	lox22_meja_1d.TechRep.2	22.2
16	caseC	two	lox22_meja_3d_TechRep.2	22.3
17	caseC	two	lox22_meja_7d_TechRep.2	24.3
18	caseC	two	lox22_meja_14d_TechRep.2	24.2

The first error I received is:
> qPCR.mine<-file.path(path, "refinedCtData2.txt")
> qPCRBatch.qPCR=read.qPCR(qPCR.mine)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 1 did not have 6 elements

I adjusted my file, but now I get this error:
> qPCR.example<-file.path("refinedCtData.txt")
> qPCRBatch.qPCR=read.qPCR(qPCR.example)
Error in .read.qPCR(filename, verbose) : 
  File incorrect, make sure that detectors are the same for all samples

However, from appearance of the file, the detectors are the same for all samples doesn't seem logical, nor intuitive. Although, 
I changed the detectors around:

Well 	Plate ID	Sample	Detector	Cq
1	caseA	one	actin_untreated_0d_TechRep.1	20.3
2	caseB	one	actin_triton_1d_TechRep.1	20.91
3	caseB	one	actin_triton_3d_TechRep.1	21.08
4	caseB	one	actin_triton_7d_TechRep.1	21
5	caseB	one	actin_triton_14d_TechRep.1	21.32
6	caseC	one	actin_meja_1d_TechRep.1	21.36
7	caseC	one	actin_meja_3d_TechRep.1	21.22
8	caseC	one	actin_meja_7d_TechRep.1	21.79
9	caseC	one	actin_meja_14d_TechRep.1	22.07
1	caseA	one	actin_untreated_0d_TechRep.2	20.1
2	caseB	one	actin_triton_1d_TechRep.2	21.1
3	caseB	one	actin_triton_3d_TechRep.2	21.12
4	caseB	one	actin_triton_7d_TechRep.2	21.3
5	caseB	one	actin_triton_14d_TechRep.2	21.21
6	caseC	one	actin_meja_1d_TechRep.2	21.5
7	caseC	one	actin_meja_3d_TechRep.1	21.4
8	caseC	one	actin_meja_7d_TechRep.2	22
9	caseC	one	actin_meja_14d_TechRep.2	22.1
10	caseA	two	lox22_untreated_0d_TechRep.1	22.28
11	caseB	two	lox22_triton_1d_TechRep.1	23.65
12	caseB	two	lox22_triton_3d_TechRep.1	24.77
13	caseB	two	lox22_triton_7d_TechRep.1	23.99
14	caseB	two	lox22_triton_14_TechRep.1	24.47
15	caseC	two	lox22_meja_1d.TechRep.1	22.13
16	caseC	two	lox22_meja_3d_TechRep.1	21.99
17	caseC	two	lox22_meja_7d_TechRep.1	24.17
18	caseC	two	lox22_meja_14d_TechRep.1	24.17
10	caseA	two	lox22_untreated_0d_TechRep.2	22.4
11	caseB	two	lox22_triton_1d_TechRep.2	23.84
12	caseB	two	lox22_triton_3d_TechRep.2	24.9
13	caseB	two	lox22_triton_7d_TechRep.2	24.2
14	caseB	two	lox22_triton_14_TechRep.2	24.6
15	caseC	two	lox22_meja_1d.TechRep.2	22.2
16	caseC	two	lox22_meja_3d_TechRep.2	22.3
17	caseC	two	lox22_meja_7d_TechRep.2	24.3
18	caseC	two	lox22_meja_14d_TechRep.2	24.2

Only to get this error message again:
> qPCR.example<-file.path(path, "refinedCtData2.txt")
> qPCRBatch.qPCR=read.qPCR(qPCR.example)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 1 did not have 6 elements

Any suggestions?

Thanks,
Franklin


 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

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

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

other attached packages:
[1] NormqPCR_1.4.0      ReadqPCR_1.4.0      affy_1.36.1         BiocInstaller_1.8.3 HTqPCR_1.12.0       limma_3.14.0       
[7] RColorBrewer_1.0-5  Biobase_2.18.0      BiocGenerics_0.4.0 

loaded via a namespace (and not attached):
[1] affyio_1.26.0         gdata_2.12.0          gplots_2.11.0         gtools_2.7.0          preprocessCore_1.20.0 stats4_2.15.1        
[7] tools_2.15.1          zlibbioc_1.4.0       
> 


--
Sent via the guest posting facility at bioconductor.org.