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This metrics uses mismatched probes on Affymetrix GeneChip arrays as internal reference for judging the hybridization of the perfect matched probes over the whole potential concentration range.
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The relative expression between matched probes was examined.
Each probe pairs contains a mismatch probe which alters its 13th position compared to a perfect matched probe.
uce-raw-genome-slices-of-probe-matches.tar: Probe + flank slices around locations matching probes targeting UCE loci.
Ambiguous and poorly matching probes were discarded from the analyses.
Two approaches to match probes across different microarray chips, annotation-based and sequence-based probe matching were used [ 6].
Therefore, for each "perfect match" probe there are 75 "mismatch" probes.
For the probes spanning the border of the annotation units, their corresponding targets only partially matched the probes, rendering those probes equivalent to the non-perfect matches.
After standard normalization of perfect match probes to the array mean, over 90% of the probes are within 1.25-fold of one another in hybridization intensity for the two parents, and these were discarded, leaving probes that are potentially mis-hybridizing to either genome due to a sequence polymorphism.
The probe match page indicates the number of probes matching the query over the total number of probes, as well as their affinity, shown as 'match'match
Non-perfect match probes had, as expected, a similar intensity distribution as probes with no match.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com