Sentence examples for microarray package and from inspiring English sources

Analysis was performed using the affylmGUI Graphical User Interface for the limma microarray package and with Partek Genomics Suite (Partek Inc., St . Louis MO, USA).

Using the Significance Analysis of Microarray package [25], we detected (at multiple testing-corrected significance q<0.01) 1274 genes differentially expressed when comparing the PFO and PT areas (PFO vs. PT) and 1763 genes when comparing samples at 17 and 19 GW individuals (17 vs. 19 GW).

The analysis was performed using the affylmGUI Graphical User Interface for the limma microarray package (Wettenhall et al, 2006).

The analysis was performed using the affylmGUI Graphical User Interface for the limma microarray package (Bioconductor Software) [ 33].

In addition, differences of the normalised expression values between treatment groups were tested using a Significant Analysis of Microarray package (SAM, Stanford University, USA) at a FDR rate of α=0.05.

To detect differentially expressed genes between fruit at harvest (S4) and after shelf-life simulation (S4+SL) in both genotypes, data were analyzed with the SAM (Significance Analysis of Microarray) package [ 30].

The differentially expressed genes were selected using a linear model approach and implemented in the Linear Models for Microarray Bioconductor package and Ingenuity's Pathway Analysis (IPA) software.

We normalized and log2-transformed the raw data, identified genes whose expressions were significantly altered in MYC2-VIGS plants (using Significance Analysis of Microarrays (SAM) package) and annotated them by Blast2Go.

The UPGMA method is equivalent to clustering algorithms implemented in popular microarray packages [ 17], whereas NJ have not been used so far, to our knowledge, in microarray studies.

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].

Differential gene expression between the groups in the initial data set and the replication data set was determined with the linear models for microarray data (limma) package and P-values were calculated with a modified t-test in conjunction with an empirical Bayes method to moderate the standard errors of the estimated log-fold changes [28].