Multivariate analysis of Pleurodeles waltl injection outcomes using FAMD FactoMineR (RStudio 4.3.2) used to probe sources of variability during an Adeno-associated viral (AAV) screen
Data files
Oct 10, 2024 version files 14.46 KB
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AAV_FAMD_final_8.14.24.R
9.04 KB
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For_Analysis_Adult_AAV_Injection_Outcomes_8.14.24_forR.csv
3.99 KB
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README.md
1.43 KB
Abstract
In this study, we analyzed the efficiency of different adeno-associated viral (AAV) injections in transfecting neurons in the salamander Pleurodeles waltl. To query sources of variation in AAV injection outcomes, we analyzed metadata and outcomes for an additional 68 intraparenchymal injections performed 39 in post-metamorphic Pleurodeles salamanders. This dataset included both quantitative variables (age, weight, viral genomes (v.g.) injected, and a cell transduction score ranging from 0 to 4, see STAR Methods) and categorical variables (here referred to as qualitative variables: serotype, promoter, reporter, single vs. dual injection, manufacturer, and injection site). To assess the associations between these variables, we performed a Factor Analysis for Mixed Data (FAMD), a principal component method that is designed to determine significant sources of variability within datasets that contain both quantitative and qualitative data types. This dataset contains the injection outcomes and metadata for AAV injections administered in the salamander Pleurodeles waltl. The RactoMineR package (https://CRAN.R-project.org/package=FactoMineR) was used to determine significant contributions of a number of variables contributing to injection outcomes. Analysis of these data revealed that, among other factors, age co-varies with injection score. Therefore, we conclude that increased animal age decreases the efficacy of this tool.
https://doi.org/10.5061/dryad.mpg4f4r89
Description of the data and file structure
This repository contains a .csv and R studio file containing the full raw metadata and code used to analyze and plot the data shown in Figure 6 and Figure S4. Within the .csv file, columns indicate metadata that may be sources of variability in a comprehensive analysis of AAV transduction efficiency. The code can be used to perform FAMD on the existing dataset and can be adapted to create similar plots in additional datasets with the same structure. Both analysis and plotting parameters are included in the script.
The headers in the .csv files with their units (if applicable) are described as follows:
age (days)
weight (grams)
single_dual: injection site contained two viruses
serotype: AAV capsid protein type
promoter: promoter used\
reporter: fluorophore used
total_virus (viral genomes)
source: manufacturer name
site: where in the brain the injection occurred
score (AU): injection outcome quality (0 no labeling-4 excellent labeling)
Acronyms:
DP - dorsal pallium
OB - olfactory bulb
Th - thalamus
Code/Software
Analysis was performed using the FactoMineR software package in RStudio 4.3.2.