I have been beginning pre-processing of a number of CEL files, basing things loosely on this tutorial and on past analysis.
That tutorial shows methods to identify chips with spatial artefacts does not seem to suggest what to do with them once identified. Should they be excluded or normalized and if there is only a small artefact is it less 'damaging' to not do the normalization? I have been having difficulty finding methods directed at spatial normalization in single-channel arrays (OLIN, smida, marray and nnNorm all seem to be written for dual-channel arrays). Can anyone please suggest an appropriate package/method for single-channel Affy chips?
Some examples of my spatial artefacts:
Of my 90 chips example 2 is the only one of that kind of pattern. The rest are mostly similar in form to the other 2 and similar patterns are seen in ~20 chips.
I really don't know much about spatial normalization on microarrays, but I am unable to see the images of your spatial artefacts to see how you might have issues. Are some areas of your microarray more intense than others? What is the extent of your spatial artefacts? Can you please update your question to clarify? Thanks!
Apologies, I have now fixed the links and elaborated a little on the extent of the problem.
Oh, yeah, I see what you mean -- looks like some awkward hybridization to me.
I am surprised at it being hard to find info on spatial normalization for single channel arrays when it seems to be a standard feature of dual channel array analysis tutorials/pipelines. Perhaps the background correction of RMA is good enough that it negates the spatial artefacts?