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We performed MATISSE analysis using the All-Neighbors heuristic, and the same parameters as in the previous section, and obtained 14 significant JACSs.
We therefore carried out all subsequent analysis using the modules produced with the All-Neighbors variant.
Analysis using the alternative classification scheme confirmed all the trends that we identified (Table S3F).
We repeated all the analysis using the median instead of the mean.
The cluster analysis used the means of all z-transformed physiological data collected during the BL, stress, and relaxation phases.
NMD = nonsense-mediated mRNA decay As it is likely that some NMD transcripts were missed from the analysis due to strict data selection, we repeated the analysis using all the RefSeq mRNAs, including predicted mRNAs (with prefix 'XM_'XM_
Then linkage analysis using all the plants in the mapping populations and polymorphic DNA markers surrounded by RM5349 and RM224 was conducted using a computer program (MapDisto ver. 1.7; Lorieux 2007).
Overall, the all phenotype analysis using all hits in the GWAS Catalogue produced the highest PPVs as the threshold for declaring a positive hit increased.
A 10 × 10 two-level nested cross-validation analysis using all the 1,863 differentially expressed genes in FFPE in present study suggested that the expression of these genes could differentiate FFPE samples from FF samples with overall accuracy of 95.7%.
Nine correlations that passed significance test were obtained by monadic regression and curve-fitting analysis using all the parameters.
We conducted two sets of analyses: a cross-sectional period analysis using all the data from 2005 2008 and longitudinal analyses using annual data from 2004 to 2008.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com