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The results were calculated based on ReCiPe end point [9], using the so-called hierarchist perspective with European normalisation data from the year 2000 [10].
The regulated gene list was consistent with both MAS5 and RMA normalisation (data not shown).
After normalisation, data were filtered to remove the spots flagged as not found.
None of the other reference genes, including Cyp, were significantly (p > 0.05) affected by IB following normalisation (data not shown).
The signal extraction model had a much larger effect on the analysis than the subsequent normalisation (data not shown).
After normalisation, data analysis yielded 9167 genes whose expression was significantly reciprocally altered in HOXD10-overexpressing and siRNA-transfected cells.
Similar(52)
Normalisations included per spot and per chip intensity-dependent (Lowess) normalisations; data transformation set measurements less than 0.01 0.01 and per chip normalisations to the 50th percentile.
The array design, normalisation and data analysis methods presented here have produced a mass of biologically relevant results (manuscript in progress).
The β2M gene was chosen for normalisation of data.
Normalisation of data is necessary for comparisons between individuals.
However, proper and highly reliable reference genes are needed for normalisation of data, as normalisation by total pathogen RNA in mixed host-pathogen samples is usually not possible.
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