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In addition to the organ marker genes, we identified a multitude of genes (6075 IDs) that were expressed at comparable levels (with a minimum expression of 6, and a range<1) in all five organs (Table S1).
Filtering by a minimum expression level obscures the influence of extreme variability of low expressed genes.
For the heat map, the cancer gene list was further filtered by requiring a minimum expression level of at least 1,000 relative fluorescence units in at least 2 different hybridizations.
We also set a minimum expression threshold of two reads per exon.
Therefore, only genes with a minimum expression change of log2 fc ≥ 0.75 during time-course were considered.
The logged original gene expression curve under warm conditions has a minimum expression level of approximately 6, which is reflected by a flat treatment-frequency expression curve with a nearly constant value of 6.
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To select a useful minimum expression threshold for validation of this method and confidant correction of gene models, we evaluated the number of FDM sequences for all gene models expressed in our data set at a range of expression levels (Figure 2).
We did this by fixing a constant minimum expression of each tested target to 1 (upregulation) or by fixing the node's state to 0 (downregulation) with a probability P GA (equal for all cells) in all cells in the lattice.
A t-test using the Benjamini-Hochberg multiple hypothesis correction (p < 0.01) and a 2-fold minimum expression change was used to identify 140 genes that were differentially expressed between cervical cancer and normal cervix.
In order to use only transcripts expressed above the noise level in the analysis, a threshold of minimum expression was fixed as the mean plus two times the standard deviation of pseudo-spots on the array that contained no cDNA sequences.
A 2.0× fold minimum expression difference was used in previous studies (Song et al. 2013; Paschold et al. 2012).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com