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Differences in stringency of data screening parameters, the taxonomic composition of databases used for the comparative analysis, and methods of phylogenetic analyses can significantly affect the outcome of the study.
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This is fewer than expected in comparison to previous reports on differential regulation during spontaneous Caco-2 differentiation and probably due to the difference in stringency of the algorithms used for data analyses (MAS 4.0 vs RMA), rather than related to functional biological discrepancies.
Cui et al [ 25] performed their study using next generation sequencing and called more regions enriched throughout the genome suggesting that the main cause of difference lies in stringency of the downstream analysis.
One possible reason for this is the difference in stringency for each motif.
This was probably due to differences in the stringency of PQS screening as well as in length of target promoter region.
This discrepancy is likely due to differences in the stringency of read alignment and quality control cutoffs, as all of the breseq indel and SNV predictions appeared to be high quality upon manual examination.
It is better given the method of analysis that examiners do not try and correct any differences in stringency, but instead they continue to behave as they have always done.
This discrepancy was mainly due to differences in the stringency of the data-processing algorithm.
FACETS allows for raw marks to be adjusted for differences in stringency between examiners.
However, it is difficult to generalise this result due to differences in stringency definition employed by each method.
This difference may be due to a difference in selection stringency of both groups.
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CEO of Professional Science Editing for Scientists @ prosciediting.com