MAplot_DE_fn

MA plot is used for visualizing the differentially expressed proteins by plotting the log mean intensity data in x axis and log fold change values in y axis.
This function can be used for visualizing the up regulated, down regulated, and non-significant proteins along with their information.

Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expression analysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluation measures were chosen for this study based on the research papers published by	Välikangas et al. (2016) <doi:10.1093/bib/bbw095>, Jin et al. (2021) <doi:10.1038/s41598-021-81279-4> and Srivastava et al. (2023) <doi:10.2174/1574893618666230223150253>.This work has published by Sakthivel et al. (2025) <doi:10.1021/acs.jproteome.4c00552>.

Kabilan S

lfproQC

Quality Control for Label-Free Proteomics Expression Data

Dr Shashi Bhushan Lal

Dr Sudhir Srivastava

Dr Krishna Kumar Chaturvedi

Dr Yasin Jeshima K

Dr Ramasubramanian V

Dr Girish Kumar Jha

MAplot_DE_fn function

<dl><dt>top_table</dt>
<dd>Top table information</dd>
<dt>x1</dt>
<dd>Cut-off limit for down-regulated proteins</dd>
<dt>x2</dt>
<dd>Cut-off limit for up-regulated proteins</dd>
<dt>p</dt>
<dd>Cut-off limit for p-values</dd></dl>

Arguments

Find out the Up and Down regulated proteins from MA plot — MAplot_DE_fn

<dl>

<dt>top_table</dt>
<dd>Top table information</dd>


<dt>x1</dt>
<dd>Cut-off limit for down-regulated proteins</dd>


<dt>x2</dt>
<dd>Cut-off limit for up-regulated proteins</dd>


<dt>p</dt>
<dd>Cut-off limit for p-values</dd>

</dl>

MAplot_DE_fn: Find out the Up and Down regulated proteins from MA plot

Description

Usage

Value

Arguments

Examples