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Probe sets which were marked absent in all array experiments were excluded from further analysis.
The data were genotyped using Illumina arrays 370, 610 and 1M, and the final list of 281 SNPs passed stringent quality control measures, including a sample call rate >96% and a SNP call rate >98% in all array types.
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If a probe has more than 35% of expression values missing in all the arrays (due to low intensities or bad flags), the expression of that probe for all the arrays is excluded for the further analysis.
Specifically the DABG p-value filter, used in this work, is designed to retain only probe sets characterized by a DABG p-value ≤ 0.05 in all the arrays.
Signal intensities and absolute calls (present, marginal or absent) measured for each probeset in all the arrays using Expression Console were recorded.
The proportion of common SNPs in all the arrays is similar (96 98%), but the GenoChip is enriched for the most common SNPs (MAF > 0.25).
To search for genes accomplishing the first condition, we kept only those that had a gene expression measurement above the 3rd quartile of the intensity distribution in all arrays.
Probes consistently expressed in all arrays were included in the analyses.
In contrast, all 10 spiking controls were grouped as differentially transcribed in all arrays.
Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Probe sets with an absent call in all arrays were removed before further analysis of the data.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com