Sentence examples for microarray analysis package from inspiring English sources

Differential expression analyses were conducted using the LIMMA (Linear Models for Microarray Analysis) package from the Bioconductor project [12].

A Bayesian moderated t-test was applied to identify differentially expressed genes as implemented in the LIMMA (linear models for microarray analysis) package [27] from Bioconductor.

Standard deviations of the logarithm of fold change values were also estimated using the limma (Linear Models for Microarray Analysis) package [41].

For data visualisation, the heat maps of gene expression were created by importing relevant subsets of RMA processed microarray gene expression data into the dChip v1.3 microarray analysis package (http://www.biostat.harvard.edu/complab/dchip/).edu/complab/dchip/

Data was normalised by variance stabilizing normalization (VSN; [78]) and differentially expressed genes were detected using the 'Limma' (Linear Models for Microarray Analysis) package [79]; implementing the empirical Bayes linear modelling approach [80].

Software implementing these methods has been included in the widely used TM4 microarray analysis package.

Some microarray analysis packages present systematically the results of several classification methods for a single data set.

Analysis of gene expression data was performed using the Bioconductor microarray analysis packages in R [ 112] and GeneSpring GX 7.3.1 (Agilent, Santa Clara, CA).

Probe-pairs from the gDNA.cel files were selected using a.cel file parser script [ 31] which produces a probe-mask file (.cdf) compatible with a range of microarray analysis packages and containing only probe-pairs in which the perfect-match probe has a gDNA hybridisation intensity greater than the user defined gDNA hybridisation threshold [ 22].

Probe pairs were identified in which the perfect match (PM) probe has a gDNA hybridization intensity greater than the user-defined threshold and were selected using a.cel file parser script (http://affymetrix.arabidopsis.info/xspecies/), which produces a probe mask file (.cdf) compatible with a range of microarray analysis packages (e.g., Genespring; Agilent Technologies).

Data was analyzed using Genespring microarray analysis software package (Agilent Technologies, Palo Alto, CA).