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The analysis was thus based upon 38.CEL files representing 22 different cell preparations and three different array platforms.
A minimal set of 54 genes that best discriminated the two subtypes was identified using the combined data sets generated from the three different array platforms.
A minimal set of genes that best discriminated the two identified subtypes were determined using PAM analysis on the combined datasets generated on the three different array platforms.
A miRNA family was included in the analysis if two or more family members appeared in at least two of the three different array comparisons.
For each of the three separate RMA runs corresponding to the three different array types, the individual perfect match (PM) probe values were background-corrected and quantile normalized before computing the expression values, as described by Irizarry et al. [ 27].
TCGA derives gene expression by extracting RNA from snap-frozen tissue and aggregating data from three different array platforms (Affymetrix U133a 2.0, Digital Gene Expression from Illumina, and a custom high-density Agilent array).
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Three different arrays of defects have been prepared with different orientations with respect to the current.
Design examples for three different arrays show that as the order number increases, the robustness of mode-beams decreases.
The complete set of chromosome 22 cDNA tiling arrays is comprised of three different arrays, numbered 1 to 3 [ 13].
A miRNA was excluded from the analysis if its expression was disconcordant across the three different arrays.
An additional 62 genes were only represented on one or two of the three different arrays used, but were defined as core genes in these experiments.
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