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The id Software gentleman said as much to CD-Action, a Polish site.
All the analyses were performed using the R (R Development Core Team, 2008) and Bioconductor software (Gentleman et al, 2004).
Affymetrix GeneChip array data were normalised, pre-processed and analysed using R and Bioconductor statistical software (Gentleman et al, 2004).
The microarray data were analyzed using the Bioconductor software (Gentleman et al 2004) designed for genomic data analysis running under the statistical programming environment R (Ihaka and Gentleman 1996).
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Data analysis was performed using the R statistical software package (Gentleman, & Ihaka, 2015) and IRT analysis was performed using the Itm package (Rizopoulos, 2006).
Data were processed using the Bioconductor software suite (Gentleman et al, 2004).
Phenotypic distribution of 11 agronomic traits were drew by boxplot function of R software (Ihaka and Gentleman 1996).
All multiplex pyrosequencing signals generated for TEM and SHV were analyzed using a new web interactive application (available at https://ucl-irec-ctma.shinyapps.io/Pyrosequencing-TEM-SHV and in 'download' section of http://www.uclouvain.be/ctma.html where a template data set can be downloaded) written with R.3.1.2 software (Ihaka and Gentleman 1996) using the "shiny" package.
Hierarchical clustering was performed using the function hcluster (package amap) of the free statistical software R (Ihaka and Gentleman, 1996).
The PCA was performed in the R software environment (Ihaka and Gentleman 1996) after normalizing the gene count in each COG category by the total gene count in the corresponding metagenome and using the R function prcomp (x, center=T, scale=T) to center the values around zero and scale to unit variance.
The heat map were described using the statistical software package R (Ihaka and Gentleman 1996).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com