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As expected, probe sets with low expression level (low signal) were less reproducible in comparisons between the different sample groups, as were probe sets with very low fold-changes.
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We expected that probe sets associated with low intensity signals would give less reliable measures of gene expression and when we removed these probe sets from the analysis the correlation improved (r = 0.90, Fig. 5B).
As would be expected, multiple probe sets spotted for the same gene will, to the extent that they induce the same partition on the samples, be assigned to the same gene set by the algorithm.
As expected, probes that comprised cis-eQTLs that were common to both data sets did not show differences in expression (P = 0.30).
Observed and expected frequencies for probe sets discovery in the three experiments alone and in the two experiments of Clarkson and Stein are given in Table 2.
In the light of recent findings that intensities of highly expressed targets cross-talk to neighbouring probes due to scanner inadequacy (cf. Upton and Harrisson, 2010), we may expect that Affymetrix probe sets contain outlying measurements.
The fitted model parameters provide information on the number of probe sets expected in each expression pattern.
In choosing the representative, we preferentially selected probe sets expected to hybridize specifically with its target, excluding those probe sets containing either an "_s_" or "_x_" suffix in the Affymetrix probe set identification number [ 79].
This simulation confirmed that again many probe sets are expected to contain one or more SNPs.
The loss of residual signal from Lbx1 probe sets is expected in null mutants.
This simulation showed that many probe sets are expected to contain one or more SNPs.
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