I'm new to affymetrix data and really need some help for my research. I have .CEL datasets from different tissues and want to calculate tissue-specificity for every gene. After reading some tutorials on bioconductor, I've know the pipeline of dealing such data, but still have some questions on details:
1) The probesets of low-quality need to be removed before calculating gene signal. Is there any packages or any standard method in Bioconductor can do this?
2) For the tissue-specificity of every gene is the goal of my work, I want to know if the gene is expressed or not in a certain sample. So how do I determine the cut-off for expression? Besides, for multiple probesets might map to one gene, how can I integrated the information from different probesets?
I've searched the keywords but got no clear solution. It will be very appreciated if anyone can help. :)