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Peter Davidsen
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210
@peter-davidsen-4584
Last seen 9.2 years ago
Dear List,
I'm trying to use the "HTqPCR" BioC package to analyze "SDS-format"
qPCR data (ran 384-well plates on an ABI 7900HT).
I have 20 different txt-files (in SDS-format) as I quantified 20
different miRNAs (thus, only one GOI per plate/file) - on each plate I
have 33 samples in triplicate.
Example of how my txt-files are organized:
SDS 2.3 AQ Results 1.0
Filename 05.08.2010_miR-208b_Ceramide_1-33
PlateID
Assay Type Absolute Quantification
Run DateTime 05/08/10 14:28:11
Operator
ThermalCycleParams
Sample Information
Well Sample Name Detector Name Reporter Task Ct....
82 D10 miR-208b FAM Unknown 31.154957
83 D11 miR-208b FAM Unknown 30.56075
84 D12 miR-208b FAM Unknown 30.617414
85 D13 miR-208b FAM Unknown 29.638447
86 D14 miR-208b FAM Unknown 29.873674
87 D15 miR-208b FAM Unknown 29.974564
88 D16 miR-208b FAM Unknown 32.324512
89 D17 miR-208b FAM Unknown 31.65119
90 D18 miR-208b FAM Unknown 32.567085
91 D19 miR-208b FAM Unknown 30.977701
92 D20 miR-208b FAM Unknown 31.459805
The command I run is:
# Load HTqPCR package
library("HTqPCR")
# Set working dir
path <- setwd('C:/Documents and
Settings/RH35363/Dokumenter/Dropbox/Ceramide Study/SDS-files')
exFiles <- read.delim(file.path(path, "files.txt")) # "files.txt"
contains a list with the file names of my 20 txt-files
raw <- readCtData(files=exFiles$File, path=path, n.features = 99, flag
= NULL, feature = 3, type = 5, position = 2,
Ct = 6, n.data = 33, na.value = 40, header=T, SDS = FALSE, skip = 10,
sep='\t') # Since my headers are apparently different/in a different
order, I have set these parameters accordingly. I've set SDS=FALSE as
my SDS software generated txt-files lack a "#" in the first column.
And the error I get is:
Error in `[<-.data.frame`(`*tmp*`, undeter, value = "Undetermined") :
only logical matrix subscripts are allowed in replacement
In addition: Warning messages:
1: In readCtData(files = "05.08.2010_miR-208b_Ceramide_1-33.txt", path
= NULL, :
99 gene names (rows) expected, got 1132
2: In matrix(sample[, Ct], ncol = n.data[i]) :
data length [116] is not a sub-multiple or multiple of the number of
columns [33]
With the traceback information as follows:
> traceback()
4: stop("only logical matrix subscripts are allowed in replacement")
3: `[<-.data.frame`(`*tmp*`, undeter, value = "Undetermined")
2: `[<-`(`*tmp*`, undeter, value = "Undetermined")
1: readCtData(files = exFiles$File, path = path, n.features = 99,
flag = NULL, feature = 3, type = 5, position = 2, Ct = 6,
n.data = 33, na.value = 40, header = T, SDS = FALSE, skip = 10,
sep = "\t")
I tried to change the "n.data" parameter from 33 to 1, this removed
the error:
raw <- readCtData(files=exFiles$File, path=path, n.features = 99, flag
= NULL, feature = 3, type = 5, position = 2,
+ Ct = 6, n.data = 1, header=T, SDS = FALSE, skip = 10, sep='\t')
Warning message:
In readCtData(files = exFiles$File, path = path, n.features = 93, :
99 gene names (rows) expected, got 1132
Thus, it seems to me like I'm loading my data in the wrong way. Any
thoughts/suggestions on how to solve this problem are welcomed!
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] HTqPCR_1.4.0 limma_3.6.9 RColorBrewer_1.0-2
Biobase_2.10.0
loaded via a namespace (and not attached):
[1] affy_1.28.1 affyio_1.18.0 gdata_2.8.2
[4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.12.0
Kind regards,
Peter
