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These include (1) investigating the effect of excluding paralogous pairs with low expressions, (2) using alternative measures of expression divergence, and (3) using several way of aggregating multiple probe data and multiple PWMs.
Before applying the SubMap, each microarray probe ID was converted into its corresponding HUGO gene symbol (http://www.gene.ucl.ac.uk/nomenclature/), and multiple probe data corresponding to a single gene symbol was averaged.
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When applied to Affymetrix microarray data, the RMA protocol improved the accuracy and precision of expression measurements compared with other methods that summarized the multiple probe level data into a gene expression measure [ 10].
By combining single probe data across multiple samples, we consider the entire population of probe expression values (gene values) as derived from a single distribution.
Although Ct can not be directly compared across multiple probe sets (in contrast to data utilizing a single probe set), the average Ct for the various probe sets (in Vec-shRNA transfectants) was as follows: ZnT8, 21.7; ZnT4, 24.5; ZnT5, 25.2; CACNA1C, 26.3; CACNA1D, 31.8; 18.0 8.0 (data set used for figures).
For genes for which there were multiple probes in the data set, the median expression value was used.
(ii) 3D gallery models can be manipulated via different similarity and affine transformations, in order to generate multiple views which fit the 2D probe data, so "2D-to-3D" matching and retrieval can be achieved. .
3D gallery models can be manipulated via different similarity and affine transformations, in order to generate multiple views which fit the 2D probe data, so "2D-to-3D" matching and retrieval can be achieved.
One difference to the CMAP database is necessitated by the multiple origins of the expression profile data represented by multiple probe ID definitions.
To interpret the microarray data, we have used multiple probe set algorithms (MAS5.0, dCHIP difference model, PLIER).
The probe data set for each gene was averaged when multiple probes were present.
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