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22 Probe sets were collapsed based on average intensity values.
We partitioned the Xl-PSIDs into equal tally and equal intensity deciles based on average intensity values in order to facilitate data analysis.
In the cases where cell somas were imaged (vPN1 imaging), fluorescence videos were segmented based on average intensity using k-means clustering, following which individual cell bodies were labeled as different region of interests.
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To identify high-quality candidates we selected 5786 genes whose variation in expression across BXD strains, based on average intensities of the genes, was higher than expected.
The genes were ranked within each dataset of PiceaGenExpress separately, based on average signal intensity in a sample type, and then equally divided into 10 intensity categories (expression classes): from the lowest 10% (class 1) to the highest 10% (class 10) (Additional file 6: Table S2, Additional file 7: Figure S4).
In the research study, the natural rainfall events were classified into three types based on average rainfall intensity and rainfall duration and the classification was found to be independent of the catchment characteristics.
(E and F ) Quantification of the NGF signaling deficit based on average fluorescence intensity of pTrk-SHC or pTrk-PLCγ immunoreactivity per cell within the neuronal population that is negative for NFH.
Material properties were assigned a-priori based on average qCT intensities at element locations.
In contrast, Fop was not correlated with gene expression, when gene expression was based on average signal intensities within a tissue type and divided in classes; but it was weakly correlated to gene expression when maximum gene expression across tissues was used (r = 0.03, P < 0.001).
Differentially expressed genes reported here, using the GeneSpring Computer Software, are based on average signal intensities indicating up- (i.e. 2-fold or greater) or down-regulation (0.5 or less) following IGF-1 treatment, as compared to untreated samples at the different time points.
To get an overview of the gene expression of 602 and NM strains induced by different culture models, hierarchical clustering was performed based on average normalised signal intensity of probes.
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