[BioC] normalisation or analysis with batch effects

[Adaikalavan Ramasamy]

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 at 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