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In contrast, microarray signals are scanned fluorescence intensities, and this translates into continuous and nearly normal expression data.
The tools described here for the simplest of microarray signals, are the foundation for further work addressing precision measures for differential expression and differentially expressed gene lists.
Since microarray signals are not quantitative at lower and higher values, signal thresholds for floor and ceiling were set for all samples.
For all genes in Groups II to IV, if the microarray signals are lower than background, the corresponding gel signals are also low (<5,000) except for three genes, HDAC5 in Group II, and DAB2 and CTSZ in Group III.
Below the threshold spike-in levels, the qPCR Ct values and microarray signals are unchanged for miR-494, while for miR-296 the Ct values increase slightly, but the array measurements are unchanged.
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The microarray signals were analyzed using the Affymetrix RMA algorithm.
Microarray signals were analysed using a rank based statistic, Rank products (RP) [11].
After 1 h incubation, unincorporated dye was removed using CentriSep spin columns (Princeton Separations, Inc .. Hybridization and detection of microarray signals was performed as described [19].
Microarray signals were determined using Affymetrix Microarray Suite 5.1.
To compare qPCR-array and microarray assays, the log2 of microarray signals was used.
Surprisingly, however, microarray signals were lower using the LNA PLP compared with the same PLP without LNA substitutes (Fig. 1).
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