Dear list, If the following question has been asked before, I do apologise in advance and hope someone can point to the relevant thread. Otherwise I would appreciate some thoughts and pointers to this problem. Thank you. Problem : My collaborator (cc-ed here) has performed hybridisation for 11 tumour and 40 normal samples on Affymetrix HGU-133Av2 (contains ~55k probesets) chips. He had hybridised about half of the samples when he realised he needed more Affymetrix chips. The second batch of chips arrived with the instruction to add DMSO in the hybridisation cocktail, which he followed. The first batch did not have such instruction. Therefore we believe that the two batches are not directly comparable. A posting to GeneArray mailing list had a reply (http://bfx.kribb.re.kr/gene-array/1255.html) supporting this view. A cross-table of batch and sample is given below : | normal tumour total batch 1 (with DMSO) | 17 6 23 batch 2 (without DMSO) | 23 5 28 -----------------------|--------------------- total | 40 11 51 Therefore I have considered the following possible solutions : 1) Preprocess all arrays and compare tumour vs. normal 2) Preprocess the two batches separately and cbind() them. Then compare tumour vs. normal 3) Preprocess all arrays but include a batch effect in analysis ( I am not sure how to do this - perhaps using LIMMA) 4) Preprocess separately and proceed as 3) Here, I use RMA to preprocess the arrays. I have done 1) and 2) and the correlation of the two gene lists, as assessed by correlation of gene ranks, is only 0.35. I think 4) is a bit of overkill. Any opinions or alternative suggestions are very welcomed. Thank you. Regards, -- Adaikalavan Ramasamy ramasamy@cancer.org.uk Centre for Statistics in Medicine http://www.ihs.ox.ac.uk/csm/ Cancer Research UK Tel : 01865 226 677 Old Road Campus, Headington, Oxford Fax : 01865 226 962