Fig. 1.

Comprehensive assessment of precision of 3,128 potential manipulation chains and comparison to the chains successfully adopted by previous studies (23, 58). On one hand, a log transformation together with the median normalization were applied before any analysis in the Table II, study 1 (23), which defined manipulation chain of that study as LOG-[NON-NON-MED]-NON. (A) The Venn diagram illustrating the number of chains (combined with five quantification tools) performing better in precision than LOG-[NON-NON-MED]-NON. (B) Significant difference in precision between LOG-[NON-NON-MED]-NON and two example chains. On the other hand, only log transformation was used to manipulate the spectral counting data from Table II, study 2 (58), the manipulation chain of which could therefore be defined as LOG-[NON-NON-NON]-NON. (C) The Venn diagram showing the number of chains (combined with four quantification tools) performing better than the chain adopted by the original study (LOG-[NON-NON-NON]-NON). (D) The significant differences were observed between LOG-[NON-NON-NON]-NON and two example chains (LOG-[MDC-RAN-LOW]-ZER and BOX-[MEC-ATO-LOW]-CEN). Each manipulation method within a chain was abbreviated by a three-letter code that was defined in Table I.