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The phrase "using the limma package" is correct and usable in written English.
It can be used when referring to the application of the limma package in statistical analysis or data processing, particularly in the context of bioinformatics.
Example: "The analysis was conducted using the limma package to identify differentially expressed genes."
Alternatives: "utilizing the limma package" or "employing the limma package".
Exact(60)
Data were imported into R software using the limma package (Smyth [2005]), transformed to the log scale (base 2), and normalized via loess smoothing with no background correction.
Significant genes were identified using the Limma package [75].
Significance testing was performed using the limma package [72].
Differentially expressed genes were identified using the limma package.
Both methods were implemented using the LIMMA package [62].
The statistical analysis was performed using the limma package.
Data exploration and quality control were performed using the Limma package.
The analysis was carried out using the limma package from Bioconductor [54].
Differential expression of the microarray data was evaluated using the limma package [81].
Differentially expressed transcripts were identified after empirical Bayesian modelling and analysis using the limma package.
The differential expression analysis was performed using the Limma package [27].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com