rlr_knn_yeast_data

This is the groupwise normalized and missing values imputed dataset of the complete yeast lysate - UPS1 benchmark dataset. 
Normalization has been done by RLR normalization method and missing values imputation has been done by KNN imputation method.

datasets

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

rlr_knn_yeast_data function

A data frame with 835 rows and 7 variables:<dl>
 <dt>Majority protein IDs</dt>
<dd>Protein ID information</dd> <dt>A1</dt>
<dd>1st sample group, 1st technical replicate</dd> <dt>A2</dt>
<dd>1st sample group, 2nd technical replicate</dd> <dt>A3</dt>
<dd>1st sample group, 3rd technical replicate</dd> <dt>B1</dt>
<dd>2nd sample group, 1st technical replicate</dd> <dt>B2</dt>
<dd>2nd sample group, 2nd technical replicate</dd> <dt>B3</dt>
<dd>2nd sample group, 3rd technical replicate</dd>
</dl>

Format

Normalized and imputed complete yeast lysate - UPS1 benchmark dataset — rlr_knn_yeast_data

A data frame with 835 rows and 7 variables:<dl>
 <dt>Majority protein IDs</dt>
<dd>Protein ID information</dd>

 <dt>A1</dt>
<dd>1st sample group, 1st technical replicate</dd>

 <dt>A2</dt>
<dd>1st sample group, 2nd technical replicate</dd>

 <dt>A3</dt>
<dd>1st sample group, 3rd technical replicate</dd>

 <dt>B1</dt>
<dd>2nd sample group, 1st technical replicate</dd>

 <dt>B2</dt>
<dd>2nd sample group, 2nd technical replicate</dd>

 <dt>B3</dt>
<dd>2nd sample group, 3rd technical replicate</dd>


</dl>

rlr_knn_yeast_data: Normalized and imputed complete yeast lysate - UPS1 benchmark dataset

Description

Usage

Arguments

Format