Hi,
I am trying to analyse the RT-qPCR datasets from Fluidigm In R in HtqPCR package and experiencing some issues creating a qPCR set. Please assist me with respect to same.
library("HTqPCR")
exPath <- system.file("exData", package = "HTqPCR")
raw <- readCtData("Assay_Plate_1.csv", path = exPath, format = "BioMark", n.features = 96, n.data = 96)
dim(raw)
n<- 96
temp<- matrix(rnorm(n*n),ncol=n,nrow=n, byrow = FALSE)
> raw2 <- new("qPCRset", exprs=temp, sampleNames = paste("S", 1:n, sep=""), featureNames = paste("A", 1:n, sep=""), featureCategory = as.data.frame(array("OK", c(n,n))), flag = as.data.frame(array("OK",c(n,n))))
Error in (function (storage.mode = c("lockedEnvironment", "environment", :
'AssayData' elements with invalid dimensions: 'featureNames' 'sampleNames'
or if I use this, i get the below error:
raw1 <- new("qPCRset", exprs = temp, featureCategory = as.data.frame(array("OK", dim=dim(temp))))
sampleNames(raw1) <- paste("S", 1:96, sep = "")
featureNames(raw1) <- paste("A", 1:96, sep = "")
Error in (function (od, vd) :
object and replacement value dimnames differ
> dimnames(raw1)
[[1]]
[1] "A1" "A2" "A3" "A4" "A5" "A6" "A7" "A8" "A9" "A10" "A11" "A12" "A13" "A14" "A15" "A16" "A17" "A18" "A19" "A20" "A21" "A22" "A23" "A24" "A25" "A26" "A27" "A28"
[29] "A29" "A30" "A31" "A32" "A33" "A34" "A35" "A36" "A37" "A38" "A39" "A40" "A41" "A42" "A43" "A44" "A45" "A46" "A47" "A48" "A49" "A50" "A51" "A52" "A53" "A54" "A55" "A56"
[57] "A57" "A58" "A59" "A60" "A61" "A62" "A63" "A64" "A65" "A66" "A67" "A68" "A69" "A70" "A71" "A72" "A73" "A74" "A75" "A76" "A77" "A78" "A79" "A80" "A81" "A82" "A83" "A84"
[85] "A85" "A86" "A87" "A88" "A89" "A90" "A91" "A92" "A93" "A94" "A95" "A96"
[[2]]
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29" "30" "31" "32" "33" "34"
[35] "35" "36" "37" "38" "39" "40" "41" "42" "43" "44" "45" "46" "47" "48" "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60" "61" "62" "63" "64" "65" "66" "67" "68"
[69] "69" "70" "71" "72" "73" "74" "75" "76" "77" "78" "79" "80" "81" "82" "83" "84" "85" "86" "87" "88" "89" "90" "91" "92" "93" "94" "95" "96"
Please assist me how to proceed.
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] HTqPCR_1.34.0 limma_3.36.3 RColorBrewer_1.1-2 Biobase_2.40.0 BiocGenerics_0.26.0
loaded via a namespace (and not attached):
[1] gtools_3.8.1 bitops_1.0-6 affy_1.58.0 stats4_3.5.1 KernSmooth_2.23-15 BiocInstaller_1.30.0 gplots_3.0.1
[8] zlibbioc_1.26.0 gdata_2.18.0 affyio_1.50.0 preprocessCore_1.42.0 tools_3.5.1 compiler_3.5.1 caTools_1.17.1.1
The same error shows up when using example data:
> library("HTqPCR")
> exPath <- system.file("exData", package = "HTqPCR")
> raw1 <- readCtData(files = "BioMark_sample.csv", path = exPath, format = "BioMark", n.features = 48, n.data = 48)
> View(raw1)
> dim(raw1)
Features Samples
48 48
> n<- 48
> temp<- matrix(rnorm(n*n),ncol=n,nrow=n, byrow = FALSE)
> raw2 <- new("qPCRset", exprs=temp, sampleNames = paste("S", 1:n, sep=""), featureNames = paste("A", 1:n, sep=""), featureCategory = as.data.frame(array("OK", c(n,n))), flag = as.data.frame(array("OK",c(n,n))))
Error in (function (storage.mode = c("lockedEnvironment", "environment", :
'AssayData' elements with invalid dimensions: 'featureNames' 'sampleNames'
I'm also experiencing this issue with trying to add data from Biomark. I've also tried manually generating matrices to create qPCRset objects, but get the same error.