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Figure 5 | Genome Biology

Figure 5

From: Detecting transcriptionally active regions using genomic tiling arrays

Figure 5

Schematic overview of the TranscriptionDetector data processing pipeline. First, a model accounting for the effect of probe sequence on non-specific binding is fit to the (log-transformed) NCP signal intensities ('step 1') and used to correct the intensity for all probes ('step 2'); a separate model is fit for each channel. For each probe, we then derive a p value reflecting the likelihood that its signal intensity belongs to the background distribution represented by the NCPs ('step 3'); these p values are calculated separately for each channel, and each channel-specific p value is treated as the outcome of an independent experiment. A multi-channel statistic equal to the product of p values across all channels is computed for each probe ('step 4'). In analogy with step 3, the distribution of this statistic for the NCPs only is then used to assign a MCPV to the other probes ('step 5'). To control for multiple hypothesis testing, a FDR procedure is used, and each probed locus is designated as transcribed or not transcribed ('step 6').

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