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For each gene, we fit a linear model with terms for probe and tissue effects.
When the latency to press a lever was analysed as the response variable (in a model containing terms for probe value, contingency group, whether the lever pressed was associated with 1 pellet or 2 pellets, their interactions, treatment group and phase), there was no significant difference, by treatment, in the latency to respond across phase (LRT = 1.91, 1 df, p = 0.167; Model 6 in ESM).
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BP terms for probes in conserved genes were enriched for transport, catabolic process and protein modification, among others (Fig. 9b).
Gene ontology (GO) terms for probes were constructed by clustering 26 plant genomes using a parallelized version of OrthoMCL according [ 28].
In terms of probe sets, our data consists of 390 probe set pairs with 201 unique probe sets.
Differentially expressed unique genes were identified in the same manner, except that probe sets with no gene annotation or with gene names including the term "hypothetical" were omitted, and for probe sets sharing the same gene annotation only the most informative ones (i.e., those with the highest interquartile range) were kept.
Given that this general model for probe summarization lacks terms for adjustment variables, and that statistical inference will be carried out on these summarized values, the goal for normalization remains the same: namely, to remove the influence of adjustment variables on probe intensities in order to maintain their true relationships with the biological variables of interest.
These ten subsets of expression probes were then analyzed for statistical enrichment of Gene Ontology (GO) terms for Biological processes using all 7,305 expressed probes as a background list.
While we did not see any significant GO term in positively correlated genes, we observed significant enrichments in 58 GO terms for 191 negatively correlated genes (200 probes).
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For probe details, see Table S2.
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