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Computational prediction was performed on a local server through batch analysis using the default parameters.
Spot finding and raw data quantification of all four microarrays for each patient were performed in a batch analysis using the MAIA® freeware.
Once again, we compared both types of analysis and two types of reference networks in batch analysis using the NOA plugin (Supplementary Fig. S7).
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during the first five days after ICU admission, centrifuged immediately and frozen at −80° for later batch analysis, using an Isotope Dilution Mass Spectroscopy traceable method (Roche Diagnostics®).
Surrogate-Variable Analysis using the ComBat algorithm was performed to reduce batch effects (Fig. S1A and B show strong dataset-specific effects prior to batch-effect removal).
(5) Perform tSNE analysis using the scores of the selected PCs using "Rtsne" function in the R package and visual inspection to assess whether there is batch effect on each cell cluster.
The instrument was calibrated for each batch of analysis using a standard mix containing des-arg bradykinin (Mr 903.47), neurotensin (Mr 1671.92), adrenocorticotrophic hormone (Mr 2464.20) and insulin-β chain (Mr 3493.65).
Of the 100 replicates in our batch processing analysis used to account for phylogenetic uncertainty, the significant diversification rate shift at the ancestor of K. antennatus, was consistently identified along the same branch although slight tree-topology changes occur among the replicate sample.
The transcription profiles for a gene set can be viewed in batch by using the analysis menu from the data-mining interface after a gene set has been selected.
Possible influence by different experimental batches or cohorts were controlled by statistical analysis using batch variables or normalizing data with Succinate dehydrogenase [ubiquinone] flavoprotein subunit (SDHA), one of endogenous controls.
Both the list derived from analysis of the 4 batches together and lists derived from single batch analysis were used and the results are summarized in tables (table S8).
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