[BioC] HTqPCR with multiple samples in multiple cards

[Ferran Briansó]

Hello,

I would like to use HTqPCR package to analyze a TLDA experiment with 4 
cards and multiple samples per card.

In concrete, I have (I) a single SDS 2.4 RQ Results file (as flat text 
file) with data from 4 SDS files corresponding with the 4 TLDA plates 
(identified as C11, C13, C15 and C9) , where on each plate I have data 
from 8 different samples (S1 to S8), and (II) another file with the 
following info (also provided in the attached file) in order to define 
the analysis layout:

mfcFileName    Sample    Infection Tissue    Condition    Color4Plots
C11    S1    CTL    A    CTL.A    grey
C11    S1    Pat1    A    Pat1.A    blue
C11    S1    Pat2    A    Pat2.A    green
C11    S1    Pat3    A    Pat3.A    red
C11    S2    CTL    A    CTL.A    grey
C11    S2    Pat1    A    Pat1.A    blue
C11    S2    Pat2    A    Pat2.A    green
C11    S2    Pat3    A    Pat3.A    red
C13    S3    CTL    B    CTL.B    grey4
C13    S3    Pat1    B    Pat1.B    blue4
C13    S3    Pat2    B    Pat2.B    green4
C13    S3    Pat3    B    Pat3.B    red4
C13    S4    CTL    B    CTL.B    grey4
C13    S4    Pat1    B    Pat1.B    blue4
C13    S4    Pat2    B    Pat2.B    green4
C13    S4    Pat3    B    Pat3.B    red4
C15    S5    CTL    A    CTL.A    grey
C15    S5    Pat1    A    Pat1.A    blue
C15    S5    Pat2    A    Pat2.A    green
C15    S5    Pat3    A    Pat3.A    red
C15    S6    CTL    B    CTL.B    grey4
C15    S6    Pat1    B    Pat1.B    blue4
C15    S6    Pat2    B    Pat2.B    green4
C15    S6    Pat3    B    Pat3.B    red4
C9    S7    CTL    B    CTL.B    grey4
C9    S7    Pat1    B    Pat1.B    blue4
C9    S7    Pat2    B    Pat2.B    green4
C9    S7    Pat3    B    Pat3.B    red4
C9    S8    CTL    A    CTL.A    grey
C9    S8    Pat1    A    Pat1.A    blue
C9    S8    Pat2    A    Pat2.A    green
C9    S8    Pat3    A    Pat3.A    red

So, I have a total of 1536 features (384 feats x 4 cards) that 
corresponds to 4 cards, with 8 samples per card and 48 features (2 
lanes) per sample.

Could anyone give me some hint on how should I use the /readCtData()/ 
and /changeCtLayout()/ functions to run the analysis? (I have already 
read the HTqPCR manual, but I have no idea on how to do it).

Thank you in advance.

-- 
Ferran Briansó
Statistics and Bioinformatics Unit (UEB)
Vall d'Hebron Research Institute (VHIR)

Passeig de la Vall d'Hebron, 119-129
08035 BARCELONA (Catalonia, Spain)
+34 934894007 // +34 934894015 (fax)
ferran.brianso at vhir.org
http://www.vhir.org