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A final set of gene expression probe-sets ready for further analysis was generated using a variance cut-off relative to the variable with the largest variance (σmax) to remove non-informative probes, set at 0.1 σ/σmax (Qlucore Omics Explorer 2.2) resulting in a final set of 24839 expression probes in the main data set.
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A variance cut-off relative to the variable with the largest variance (σmax) was used to remove noninformative probes; this was set at 0.05 σ/ σmax (Qlucore Omics Explorer 2.2).
A standard unsupervised hierarchical cluster analysis (HCA), after using a variance filter with a cut-off value of 50% of the highest standard deviating genes to limit the number of probes and a Pearson correlation test [ 20] for average linkage clustering, was used to investigate similarities and differences in global gene and miRNA expression patterns among disomy 8, trisomy 8, and references.
We assigned a cut-off value, using a variance analysis, to the microarray slide.
We performed sensitivity analyses using a 14-day cut-off.
Significance was determined using a 5% FDR cut-off.
After blast, GO annotation was performed using an e-value cut-off of 1e−03, an annotation score cut-off of 45, and a GO weight of 5.
The presence or absence of a cut-off value effect is now more formally investigated using a covariate cut-off, which is zero when the summary score with a cut-off value of 10 is used and one otherwise.
The manufacturer's recommended cut-off index value of 1.1 was used to define seropositivity; sensitivity analyses using a higher cut-off were also conducted as described below.
The power of detection was on average 97% using a 70% cut-off and 94.2% with 90% cut-off for identifying conflicting bipartitions, while the rate of false positives was below 4.2%and2.1%1% for the two cut-offs, respectively.
To do so, the group was randomized using an Euroscore II cut-off point of 10.
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