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We have integrated the sequence database with the microarray data so that each microarray feature is linked to the sequence database for the corresponding CloneID.
Because BGIBMGA002049 has no information in microarray data, so it was not included in the study.
The Kimmel lab has considerable experience, over several years, with microarray data so the expertise of his team to evaluate and write such an article is well placed.
However, in contrast to work performed on expression microarray data, so far there has been no detailed assessment of the effects of different parameters or of enrichment assays on the overall results from these methods.
These genes were selected on the basis of gene-level Brainarray summaries [ 18] of the Exon 1.0 microarray data, so exon-level and splicing information were not taken into account.
Connector C5 transforms one-color microarray data into (virtual) two-color microarray data, so they can be processed by RGUI, while connector C6 filters the produced differential gene expression data, so they can be analysed by DAVID.
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There are some other function modules, e.g. a cis-element significance analysis toolbox for gene promoter sequences, an expression pattern search for microarray expression data so users can compare gene expression differences in various growth periods or under diverse stresses.
Those interested in using the original microarray data can do so, and perform their own comparison and analysis.
First, the log10 microarray data were normalized so that signals for one of the spike-ins (E1A_r60_a20) with a log relative concentration of 3.83 had the same values across all samples.
Unlike the conventional theoretical methods, which always give a single mathematical model for cancer network for a more detailed theoretical analysis, this study is to introduce a systems biology approach to cancer network markers based on real microarray data through the so-called reverse engineering, theoretical statistical method and data mining method in combination with big databases.
The microarray data was log-transformed so that it would be on the same scale as the ΔCT values.
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