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Question: Creating a qPCRset object from a text file
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gravatar for s.m.may
5 weeks ago by
s.m.may0
s.m.may0 wrote:

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

ADD COMMENTlink modified 5 weeks ago by valery.sherina10 • written 5 weeks ago by s.m.may0
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gravatar for valery.sherina
5 weeks ago by
United States
valery.sherina10 wrote:

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

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by valery.sherina10

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.

ADD REPLYlink written 5 weeks ago by valery.sherina10
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