Hi, I'm just trying to migrate from cellHTS1 to cellHTS2 and I wonder if somebody could answer me some questions around the new structure of the object. If x is a cellHTS2 object created with: x <- readPlateList("platelist2.txt", name = expName, path = dataPath) from a platelist file that look a bit like: Filename Plate Replicate Channel Batch 1a1.before 1 1 1 1 1a2.before 1 2 1 1 1b1.before 2 1 1 1 1b2.before 2 2 1 1 2a1.before 3 1 1 1 2a2.before 3 2 1 1 2b1.before 4 1 1 2 2b2.before 4 2 1 2 where the different batches represent plates processed by different experimenters. The complete set have 18 plates, with 2 replicates and 2 channels. The plates are divided into 6 batches. and configured with a plate configuration file like: Wells: 96 Plates: 18 Plate Well Content * * sample * A01 neg1 * B01 neg1 * C01 siCasp8 * D01 siCasp8 * E01 siCasp8 * F01 siBid * G01 siBid * H01 siBid * A12 empty * B12 empty * C12 nt * D12 nt * E12 siKif11 * F12 siKif11 * G12 neg2 * H12 neg2 channels are normalised with xn<-summarizeChannels(x,fun = function (r1,r2) r2/r1) and plate normalised with xnp <- normalizePlates(xn, scale = "multiplicative", log = TRUE, method = "median", varianceAdjust = "none") How would I perform tasks such as 1)producing a mean/sd for each type of control well for each plate (with separate replicates of the same plate being counted separately), and each batch (to look for differences between batches). 2) Plot the correlation between the two replicates for each batch to find if one batch is more variable than any other. 3) Produce box plots for the sample values in each plate (again plates in different replicates treated as different plates) so that different normalization methods can be compared. 4)Average over the values for each well in every plate (i.e. all of the A01s or all of the B05s), output as a 8x12 matrix so that a plot can be produced to look for edge effects in the plates. I'm having a little trouble getting to grips with the more complex structure of cellHTS2 as compared to cellHTS1. Cheers, Ian Sudbery ------------ Wellcome Trust Sanger Institute. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.