Manual creation of qPCRset does not work
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Ed Siefker ▴ 230
@ed-siefker-5136
Last seen 3 months ago
United States

Trying to build a qPCRset, and found example code here and more recently here:

mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96,  byrow = FALSE)
raw <- new("qPCRset", exprs = mat, featureCategory =
as.data.frame(array("OK",  dim=dim(mat))))
sampleNames(raw) <- paste("S", 1:6, sep = "")
featureNames(raw) <- paste("A", 1:96, sep = "")

This code does not work.

> mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96,  byrow = FALSE)
> raw <- new("qPCRset", exprs = mat, featureCategory =
+ as.data.frame(array("OK",  dim=dim(mat))))
> sampleNames(raw) <- paste("S", 1:6, sep = "")
Error in (function (od, vd)  : 
  object and replacement value dimnames differ
> featureNames(raw) <- paste("A", 1:96, sep = "")

I did correct the typo in the matrix() call, but this had no effects on assigning sampleNames(). The error appears to be incorrect. Both the object and replacement dimnames are NULL.

> dimnames(sampleNames(raw))
NULL
> dimnames(paste("S", 1:6, sep = ""))
NULL
> 

Does anyone have working code to manually create a qPCRset?

bug nondetects HTqPCR • 472 views
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@james-w-macdonald-5106
Last seen 48 minutes ago
United States
> mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96,  byrow = FALSE)
> pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names = paste0("S", 1:6)), varMetadata = data.frame(labelDescription = "Sample numbering", row.names = "Sample names"))
> fd <- new("AnnotatedDataFrame", data = data.frame(featureNames = paste0("A", 1:96), varMetadata = data.frame(labelDescription = "Super fakeo")))
> fc <- as.data.frame(array("OK",  dim=dim(mat)))
> raw <- new("qPCRset", exprs = mat, phenoData = pd, featureData = fd, featureCategory = fc)
> raw
An object of class "qPCRset"
Size:  96 features, 6 samples
Feature types:        
Feature names:       A1 A2 A3 ...
Feature classes:          
Feature categories:  OK 
Sample names:        S1 S2 S3 ...
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Thanks! This works for me.

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How do we feed in the data from a data frame containing our Ct values into this object? That's the part I am stuck on, sorry if that's an obvious question (I am new to R and using this package).

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The answer I provided above explains exactly how to do that, with the exception of needing to coerce a data.frame to a matrix.

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Ah sorry yes, my question was not specific enough (again, new to R and programming in general), but what you have said makes sense,

"coerce a data.frame to a matrix." I'll look into how to do that, thanks.

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