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 Brians? 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