Evening,
I have a txt file with 26 samples(rows ) with 30 microRNA (coloumns) - how do I convert this into qPCRset object to do further analysis on the"nondetect" R package?
Thanks
Shaun
Dear Shaun,
Thank you for your interest in nondetects.
Similar question was addressed here: HT qPCR; Creating qPCRset from expression matrix
You would need to create a qpcr set object yourself.
mat <- matrix(rnorm(9*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 = "")
In the vignettes for HTqPCR package "qPCR analysis in R" you can find additional information on how to add phenoData https://bioconductor.org/packages/release/bioc/html/HTqPCR.html
I hope this helps, and please let me know if you need more help with creating a qPCR set object.
Best,
Valeriia
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version 2.3.6
The package nondetecs requires you to have replicate samples, i.e. treatment (samples 1 - sample 3) vs control (sample 4 - sample 6). In nondetects package the qPCR set object has genes as rows and samples as columns, with replicate information.