One remaining challenge for the processing of ChIP-seq data is the mapping of ambiguous tags.
Processing of ChIP-chip data was performed in three steps: normalization, IP/mock-IP ratio computation (in log2 scale) and enriched-region identification.
To overcome these problems and determine the actual protein-binding sites to within a few 10 bp, algorithms for the processing of ChIP-seq data have been proposed, although the results obtained by them are still predictive.
The most similar existing package, CisGenome [ 1], provides a greater emphasis on processing of raw ChIP-Chip and ChIP-Seq data and peak-finding, but is limited with respect to the scope and ease of use of the motif and data visualization and analysis options.
Batch effects can be subdivided into two types, those that happen during manufacturing of the chip and those that happen during the processing of the chip.
For nucleic acid detection the processing of the chip will differ only in the technical details required for the specific method of amplification.
It is likely that more intense selection for the high starch content and low reducing sugar content required in processing of the Chip Processing lines vs. the French Fry Processing lines has contributed to these differences.
From the traditional conformal coatings used to protect printed wiring boards and insulate wire, coatings are now used as high performance dielectrics as an integral step in the processing of semiconductor chips, multichip module interconnect substrates, flip-chip devices, and ball-grid-array packages.
The procedure for the microarray experiment has previously been published.[ 19] All microarray chips and related protocols and equipment for the processing of these chips were from Affymetrix Inc., Santa Clara, CA. The human genome GeneChip U133A consisting of more than 22000 probe sets was used for this study.
The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2407/10/222/prepub wishish to thank Cécile Reyes and Benoit Albaud, from the Affymetrix Platform of the Institut Curie, for their help in the production and the processing of the chips, Blandine Massemin and Michèle Galut for their help in the processing of DNA and RNA samples.
