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We have conducted a correlation analysis to determine the agreement in the estimated gene expression fold changes (log2 thereof) obtained with high-throughput expression profiling techniques and qRT-PCR.
The second strategy overcomes this shortcoming, although the estimated gene expression stabilities may include some errors (Guenin et al. 2009).
The estimated gene expression was calculated as 2−ΔΔCt and statistical significance was estimated using the Student's t-test.
Therefore, such probes were more likely to be selected by our probe selection algorithm, increasing the estimated gene expression indexes.
As shown in table S2, estimated gene expression changes may differ among the different probesets that are available in the array for each gene.
Nevertheless, other biases caused by the sequencing process, such as a GC-content dependent production of reads [20], could also have a substantial effect on the estimated gene expression levels and these are not considered here.
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Apart from RT-PCR studies, databases containing expressed sequence tags (ESTs) can be used to estimate gene expression.
MPSS is an alternative technology that estimates gene expression by counting short sequence signatures generated from up to one million expressed sequences per run.
We then counted the reads to estimate gene expression level from mapping results of F1 to the pseudo-reference.
This correlation provides strong experimental support for the application of mgMOS for estimating gene expression level from microarray data.
The gene expression data used to estimate gene expression in ovarian tumors included cDNA microarray profiles of 72 ovarian tumors, of which most were late stage tumors of serous histology (manuscript in preparation).
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