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Extractive measurements were performed in the flame using an oil-cooled particle extraction probe.
RNA extraction, probe preparation, and array hybridizations were all carried out at the Rosetta Inpharmatics Gene Expression Laboratory (Seattle, WA).
RNA extraction, probe labelling and hybridization were performed as previously described [ 42].
Details for RNA extraction, probe synthesis, hybridization on oligonucleotide arrays and statistical analyses are provided as Supporting Information.
Plant growth conditions, RNA extraction, probe synthesis, and array hybridization were carried out as described previously (Matsui et al. 2008; Kurihara et al. 2009).
To minimize technical variability, RNA processing steps (RNA extraction, probe labelling and chip hybridization) were performed in parallel for control and asthmatic samples.
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Plants were hand pollinated and ovules were collected between 0 and 22 days after pollination (DAP) and used for RNA extraction and probe preparations.
After applying multiple background, intra- and inter-array effect corrections and signal extraction and probe summarisation techniques, we demonstrate the factors affecting the concordance of both magnitude and statistical significance of the transcriptomic effects between platforms.
In SNEP analysis, extraction of probes sets does not affect on individual SFP detection performance, because SNEP analysis performs SFP detection on a set by set basis.
To obtain gene expression measurements, the extraction of probe-level data was performed with a standard GC-RMA algorithm for background correction and summarization steps and least-variant set algorithm for normalization based on a least-variant set of probe sets.
In feature extraction, PM probes for the sense strand of allele A (PMA) are corrected for the noise of non-specific hybridisation by averaging the mis-match values of both alleles (A and B) on the sense strand [ MMA + MMB /2] and subtracting this from the PMA value.
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