[BioC] HTqPCR problem

[Heidi Dvinge]

Dear Sandra,

> Hello:
>
> I have faced a problem when I´m trying to analyze my TLDA data:
>
> I have 3 or 2 technical replicates per sample, my problem is that I really
> don´t know how to read and asses the replicates.
> What I tried is to analyze my data as individual samples and then asses
> the replicates as  following:
>
> d.normA2= exprs(d.normA)
>> d.normA2.prom= (d.normA2[,1]+ d.normA[,2]+ d.normA2[,3])/3)
>> d.normA2.prom= cbind(d.normA2.prom,(d.normA2[,4]
> + d.normA2[,5]+ d.normA2[,6])/3)
>> d.normA2.prom= cbind(d.normA2.prom,(d.normA2[,11]
> + d.normA2[,12]) + d.normaA2[,13])/3)
>
> But I get: Error: inesperado ')' en "d.normA2.prom= (d.normA2[,1]+
> d.normA[,2]+ d.normA2[,3])/3)"
>
This is just telling you that you have an unmatched ")", i.e. the last
parenthesis after /3 isn't required.

More importantly though, what are you trying to do with these objects? If
d.normA is a qPCRset object containing all 74 arrays, then there are
different ways you can perform quality control. For example, you can
cluster all samples is see if the replicate samples cluster together
(plotCtPCA, clusterCt).

If you want to compare just 2 arrays, you can use e.g. plotCtScatter to
estimate how much they vary. plotCtPairs can be used for >2 arrays,
although the plot will be too nitty-gritty with all 74 arrays.

Alternatively, there's a new function, plotCtVar, that will make a boxplot
of the variation across replicates of all 30 samples individually, to
asses if the replicates vary more for some samples than others. I don't
think I've added plotCtVar to the development version of HTqPCR yet, but I
can email it to you if that's any help.

Alternatively, if your d.normA object does not contain data from all 74
arrays, or if it's some kind of different comparison of your replicates
that you're after, then try emailing some of your code and/or a longer
description of what you're trying to achieve,

HTH
\Heidi

> I don´t know which is the best option to read my replicates because I´m
> trying to evaluate 74 TLDA files corresponding to 30 samples, with
> technical replicates.
>
> Thank you a lot.
>
> Biol. Sandra Lorena Romero Córdoba
> Ph student at Autonomous National University of Mexico
> Lab. Genomics of Cancer, National Institute of Genomic Medicine
> 	[[alternative HTML version deleted]]
>
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