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3-D printing tipping point?
Contamination of printing tips and non-specific binding of DNA to slide surface was controlled by spotting water and buffer in 244 spots.
For within array and between array normalization, print tip Loess and scale was used.
The data was normalized using the print tip loess method as described in the methods section.
Gene expression was quantified with the SMA package using print tip group lowess normalization without background subtraction [42], [43].
Intra slide and inter slide normalization were performed using the Print Tip Loess and the quantile methods respectively.
The expression ratios were normalized without background correction using the print tip loess method [31] of the limma package [32] from Bioconductor.
Data were expressed as log2 intensity ratios (Cy5/Cy3), normalized with a print tip locally weighted linear regression (Lowess) method and filtered based on spot quality and incomplete annotation.
The dataset developed by Tomlins et al. [11] was downloaded from the GEO database and raw data normalized using print tip normalization.
Log-transformed ratios of mean foreground intensities (not background corrected) were print tip loess normalised.
Intra- and interslide normalization was performed using the Print Tip Loess and the quantile methods, respectively.
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