Sentence examples for using the affyPLM package from inspiring English sources

Array quality was analyzed using the affyPLM package [58].

Data quality was assessed using the affyPLM package for the R programming language.

Additionally, the quality of the arrays was assessed based on Relative Log-Likelihood (RLE) and Normalised Unscaled Standard Errors (NUSE) criteria generated using the "affyPLM" package in the R open-source software.

Further quality diagnostics were based on the fit of a probe level model to the data, implemented using the affyPLM package [35], which models the dependence of probeset intensities on the probes and the array using robust regression procedures [36].

The quality of the hybridization reactions was checked using the affyPLM package.

Quality control of the array data was performed through Bioconductor (2.14) in the R statistical environment (version 3.1.0) using the affyPLM package [ 33].

Array quality was assessed by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM Bioconductor package (version 1.34.0); all arrays had median RLE and NUSE values less than 0.1 and 1.05, respectively, indicating that they were of sufficient quality.

Microarray quality-control assessment was carried out using the AffyPLM R-package [ 32].

The quality of microarray images from individual chips was examined using methods from the affyPLM package of Bioconductor http://www.Bioconductor.org[ 60].

NUSE, [ 25] was determined by probe level modelling using the Bioconductor AffyPLM package, see Materials and Methods; IQR, interquartile range.

Microarray quality-control assessment was carried out using the R AffyPLM package available from the Bioconductor web site (, [ 50]).