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The mean probe fluorescence (FL1) normalized by DNA fluorescence (FL3) and the median fluorescence (MFL1) weighted by percentage of probe-binding particles (FL1 positives) were analyzed.
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mean probe delay.
Probe fluorescence was read using a Luminex detection platform.
For all treatments, the number of undetected microarray probes (mean fluorescence intensity less than two times the mean local background intensity in all tissue-types and replications) in each chickpea genotype varied according to the source of the probes.
To avoid quenching of fluorescence signal within other probes, fluorescence and dabcyl (quencher) positions of Alexa488-probe were switched.
To exclude poor-quality probes from statistical analyses, hybridisation success and mean fluorescence for each probe were evaluated in a total of 31 experiments (four biological replicates for each developmental stage with the exception of 13 dph, for which one biological replicate was discarded).
Gene-level analyses were performed using the mean normalized fluorescence values for all probes and replicates.
Probes are also distinguished according to the mean fluorescence value of the probe showing the lower signal (FLS, Fluorescence Lower Signal).
For An. gambiae, only probes that had a mean fluorescence intensity across all 13 timepoints >20 were analyzed.
Class assignment was conducted by considering the mean fluorescence value of the probe showing the lower signal for each pair comparison.
In order to compensate for variations in amounts of RNA deposited in spots, normalization was performed by dividing the background corrected mean fluorescence intensity of target cDNA probe (Cy3 channel) by background corrected mean fluorescence intensity of the house-keeping gene (18S rRNA) probe (Cy5 channel).
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