Sample grouping (phenoData) and visualization in R package- HtqPCR
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@mohammedtoufiq91-17679
Last seen 5 weeks ago
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Hi,

I created a qPCRset using HTqPCR package for analysing the RTPCR data from BioMark Fluidigm setup. I am facing issues while grouping the samples for the data visualization and analysis. I would like to group the samples based on the "Type" parameter such as 1, 4, and 6. However, getting an error message. Below is the code and error message

library("HTqPCR")

expression <- read.csv(file = "/Users/mtoufiq/Library/R/3.5/library/HTqPCR/exData/BMT_CSV.csv", stringsAsFactors = FALSE)

expression[is.na(expression)] <- 0

expression <- data.matrix(expression[,-1])

dd <- data.frame(expression)

mm1 <- as.matrix(dd)

mm2 <- matrix(mm1, ncol = ncol(dd), dimnames = NULL)

dim(mm2)

raw <- new("qPCRset", exprs = mm2, featureCategory = as.data.frame(array("OK", dim=dim(mm2))))

sampleNames(raw) <- paste("S", 1:27, sep = "")

featureNames(raw) <- paste("A", 1:265, sep = "")

pData(raw) <- data.frame(Patient=c(rep("Patient1", 7), rep("Patient4", 9), rep("Patient_6", 11)), Type=c(rep("1", 7), rep("4", 9), rep("6", 11)))

pData(raw)

g<- featureNames(raw)[1:10]

plotCtOverview(raw, genes=g, xlim=c(0,90))

plotCtOverview(raw, genes=g, xlim=c(0,50), groups=Type)

pData(raw)

 Patient Type

1 Patient_1 1

2 Patient_1 1

3 Patient_1 1

4 Patient_1 1

5 Patient_1 1

6 Patient_1 1

7 Patient_1 1

8 Patient_4 4

9 Patient_4 4

10 Patient_4 4

11 Patient_4 4

12 Patient_4 4

13 Patient_4 4

14 Patient_4 4

15 Patient_4 4

16 Patient_4 4

17 Patient_6 6

18 Patient_6 6

19 Patient_6 6

20 Patient_6 6

21 Patient_6 6

22 Patient_6 6

23 Patient_6 6

24 Patient_6 6

25 Patient_6 6

26 Patient_6 6

27 Patient_6 6

plotCtOverview(raw, genes=g, xlim=c(0,50), groups=Type)

Error in plotCtOverview(raw, genes = g, xlim = c(0, 50), groups = Type) : object 'Type' not found

sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.14.5

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] C

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

other attached packages: [1] HTqPCR1.36.0 limma3.38.3 RColorBrewer1.1-2 Biobase2.42.0 BiocGenerics_0.28.0

loaded via a namespace (and not attached): [1] gtools3.8.1 bitops1.0-6 affy1.60.0 stats43.5.1
[5] KernSmooth2.23-15 gplots3.0.1.1 zlibbioc1.28.0 gdata2.18.0
[9] affyio1.52.0 preprocessCore1.44.0 tools3.5.1 yaml2.2.0
[13] compiler3.5.1 BiocManager1.30.4 caTools_1.17.1.2

HtqPCR grouping visualization R phenoData • 241 views
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