[BioC] miRNA exiqon panels and HTqPCR

[Heidi Dvinge]

Hi Eli (sorry, accidentally pressed "Send" too soon),

> Dear Heidi,
>
> I want to analyse my data from miRNA exiqon panels with HTqPCR. but I'm
very new using Bioconductor. I read pdf from HTqPCR but I don't know how
to prepare my samples.txt. I analyze 24 samples (10 treatment A, 8
treatment B, 5 without treatment and 1 as negative control qPCR) with
miRNA panel I and II LNA qPCR from exiqon. For any sample I have 768
miRNA evaluated.
>
> My questions are:
>
> - I need one .txt for any sample and panel with Ct information for any
miRNA. Then I have to combine panel I and II for any sample with cbind
or I can use a .txt with Ct for 768 miRNA?
>
You can indeed use a text file for all 768 miRNAs, rather than processing
each miRNA individually (that would be rather tedious). Depending on how
you currently have your data, the process can be:

1) All your 24 samples are in separate files. Read in the data with:
readCtData(files=c("filename1.txt", "filename2.txt", "filename3.txt",
...), n.features=768, ...)
2) All your 24 samples are concatenated together into the same file, i.e.
it contains 24*768 rows:
readCtData(files="combined_file.txt", n.features=768, n.data=24, ...)

Obviously, the your file names can be called whatever you want them to;
these are just examples for simplicity.

> - Each .txt must have miRNA name and Ct value, anything else?
>
That's the minimum amount of information required. However, if you want,
you can include more information, such as location of the miRNA on the
plate (e.g. A1, A2, ...), some quality information from the plate reader
(e.g. whether the well on the plate passed or failed the quality control)
etc.

> - Moreover .txt for each sample I need a .txt with samples names and
group? 
>
You'll need some sort of mapping between your file names and what they
contain. Maybe you already have a file that has e.g. columns for
"SampleID" and "Group", and you can just read that file into R with
read.table. Or you can just input that information into R yourself, such
as:

sample.info <- data.frame(Sample=paste("sample", 1:24, sep=""),
Group=rep(c("A", "B", "NO", "Cnt"), c(8,10,5,1)))

> Thank you for your help
>
HTH
\Heidi

P.S. Please note that I'm cc'ing the Bioconductor mailing list, since
that's the official forum and repository for questions regarding
Bioconductor packages.

> Eli