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These results provide reassurance that VBM studies comparing groups are not vulnerable to the higher than expected false positive rates that are evident in single case VBM.
An ANOVA analysis was used to identify genes with significant differences in expression, with a P-value cut-off of 0.05, indicating 284 expected false positive genes.
As in the BXD analysis, the yield of suggestive QTLs is above the expected false positive rate (one per genomewide scan).
To achieve an 80% power to detect a gene expression difference of 2-fold and above, we will need 18 pairs of samples, assuming a set of 1,145 human miRNA genes on the microarray, a standard deviation of 0.7, 1 expected false positive, and an adjusted P-value of 0.001 (http://bioinformatics.mdanderson.org/MicroarraySampleSize).org/MicroarraySampleSize
> We estimated the number of expected false positive mappings that passed our criteria.
This indicates for both datasets that the number of significant tests is not explainable by the expected false positive rate.
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Q values were calculated from p values of all 862 genes, and q-value-based significance analysis suggested that the expected false positives are only four genes out of this list.
FDR describes the number of expected false positives among all positive findings at a certain p-value threshold [18].
In order to estimate the number of expected false positives due to multiple testing of sites, a false discovery rate (FDR) was calculated for each model using 1,095 random SNPs throughout the genome.
The cut-offs values corresponded to four expected false positives for each clone list.
The number of differentially expressed protein spots in both studies is below the number of expected false positives.
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