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Fig. 2 | BMC Genomics

Fig. 2

From: A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray

Fig. 2

Platform evaluation. a Pre-processing methods were evaluated on the whole array using the titration response as a function of the fold-change between samples A and B. Probesets were binned according to the fold-change values between A and B. Unlike GCBG-RMA, the three methods RMA-TPRN, RMA and Li-Wong present narrow titration curves, indicative of good performances. The two confounding factors (b) intensity and (c, same colour code as in 2b) probeset size distribution are represented in HERVs/MaLRs, gU133/gHTA and gPEHM compartments: the intensities are lower in HERVs/MaLRs than in genes (gPEHM, gU133/gHTA), reffecting a smaller proportion of expressed loci in the former. The three compartments, HERVs/MaLRs, gU133/gHTA, gPEHM, and downsized gPEHM (dgPEHM) are compared on (d) repeatability (CV) and accuracy measured both by (e) the titration response and (f) the estimated dilution mixture (\( {\widehat{\beta}}_{\mathrm{C}},{\widehat{\beta}}_{\mathrm{D}} \)). The grey horizontal lines in (f) symbolizes the theoretical mixture values β C and β D. Only probesets differentially expressed between samples A and B (fold-change A/B and B/A > 2, P < 0.01) were used to generate the boxplots in (f). The gene repertoires show similar level of repeatability and accuracy (similar median CVs, titration curves and \( {\widehat{\beta}}_{\mathrm{C}},{\widehat{\beta}}_{\mathrm{D}} \) distributions), whereas HERVs/MaLRs performances are slightly lower, due to smaller probesets

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