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Hybridizations resulting in a "present" flag using the Agilent Feature Extraction 9.5.1 software were considered successful.
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Genes in the GDS1813 dataset were filtered by requiring a "present" flag in at least 30 out of 52 samples.
A present flag was given to every gene that is marked as present in at least three out of four experiments.
Gene list U was generated by MAS5 including genes with >2-fold difference between parental and PPP treated cells and giving a "present" detection flag in both cell lines (Uppsala Array Platform).
Each microarray was subjected to a standard quality control evaluation; the percentage of probe sets reliably detected (present flag) in each array was between 39.4% and 54.8%, and the 3′/5′ ratios for GAPDH and 18S rRNA gene were less than 5.25 and 2.19, respectively.
Only a probe that had present flags in at least 50% samples of all the arrays was kept for further analysis.
Only a probe that had present flags in at least 50% samples of all the arrays was kept for further analyses.
Probes with present flags in all of the technical replicates for at least one biological condition in a given study were retained in the data set for that study.
Among 55 K genes on the microarray, only the genes with present flags in at least 50% of samples were selected for subsequent analysis.
Article 45 of the Paris Convention (1858) provided that "the armies of both countries will keep their present flags; but these flags will feature, in the future, a blue banderole, in conformity with the design attached to the present Convention".
Probes showing a "present" or "marginal" flag call in 100% of the samples in any one of the 5 time points were considered reliably expressed (13,517 probes).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com