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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
>
--
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