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PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.

Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA - PLoS ONE (2015)

Bottom Line: PhenStat is targeted to two user groups: small-scale users who wish to interact and test data from large resources and large-scale users who require an automated statistical analysis pipeline.The package was tested on mouse and rat data and is used by the International Mouse Phenotyping Consortium (IMPC).By providing raw data and the version of PhenStat used, resources like the IMPC give users the ability to replicate and explore results within their own computing environment.

View Article: PubMed Central - PubMed

Affiliation: The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

ABSTRACT
The lack of reproducibility with animal phenotyping experiments is a growing concern among the biomedical community. One contributing factor is the inadequate description of statistical analysis methods that prevents researchers from replicating results even when the original data are provided. Here we present PhenStat--a freely available R package that provides a variety of statistical methods for the identification of phenotypic associations. The methods have been developed for high throughput phenotyping pipelines implemented across various experimental designs with an emphasis on managing temporal variation. PhenStat is targeted to two user groups: small-scale users who wish to interact and test data from large resources and large-scale users who require an automated statistical analysis pipeline. The software provides guidance to the user for selecting appropriate analysis methods based on the dataset and is designed to allow for additions and modifications as needed. The package was tested on mouse and rat data and is used by the International Mouse Phenotyping Consortium (IMPC). By providing raw data and the version of PhenStat used, resources like the IMPC give users the ability to replicate and explore results within their own computing environment.

No MeSH data available.


Related in: MedlinePlus

Example output of the PhenStat scatterplotGenotypeSexBatch function.Shown is the variation with batch in the peak contracture pressure readings for rats from SS strain (coloured in black) compared to the SS-3BN/Mcwi strain (coloured in red) visualised using the scatterplotGenotypeSexBatch function. This plot allows the user to visualize the batch variation and assess how the treatment effect compares to the observed batch variation. It is important to note that as dates can be entered in many forms, the batches are not ordered with time.
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pone.0131274.g006: Example output of the PhenStat scatterplotGenotypeSexBatch function.Shown is the variation with batch in the peak contracture pressure readings for rats from SS strain (coloured in black) compared to the SS-3BN/Mcwi strain (coloured in red) visualised using the scatterplotGenotypeSexBatch function. This plot allows the user to visualize the batch variation and assess how the treatment effect compares to the observed batch variation. It is important to note that as dates can be entered in many forms, the batches are not ordered with time.

Mentions: The dataset (S1 Dataset) was processed using PhenStat V2.0.1 and the code available in the Supplementary Information (S1 Code). Exploration of raw data (Fig 5 and Fig 6) highlights a visual difference in the variable of interest that could potentially be attributed to the genotype change.


PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.

Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA - PLoS ONE (2015)

Example output of the PhenStat scatterplotGenotypeSexBatch function.Shown is the variation with batch in the peak contracture pressure readings for rats from SS strain (coloured in black) compared to the SS-3BN/Mcwi strain (coloured in red) visualised using the scatterplotGenotypeSexBatch function. This plot allows the user to visualize the batch variation and assess how the treatment effect compares to the observed batch variation. It is important to note that as dates can be entered in many forms, the batches are not ordered with time.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493137&req=5

pone.0131274.g006: Example output of the PhenStat scatterplotGenotypeSexBatch function.Shown is the variation with batch in the peak contracture pressure readings for rats from SS strain (coloured in black) compared to the SS-3BN/Mcwi strain (coloured in red) visualised using the scatterplotGenotypeSexBatch function. This plot allows the user to visualize the batch variation and assess how the treatment effect compares to the observed batch variation. It is important to note that as dates can be entered in many forms, the batches are not ordered with time.
Mentions: The dataset (S1 Dataset) was processed using PhenStat V2.0.1 and the code available in the Supplementary Information (S1 Code). Exploration of raw data (Fig 5 and Fig 6) highlights a visual difference in the variable of interest that could potentially be attributed to the genotype change.

Bottom Line: PhenStat is targeted to two user groups: small-scale users who wish to interact and test data from large resources and large-scale users who require an automated statistical analysis pipeline.The package was tested on mouse and rat data and is used by the International Mouse Phenotyping Consortium (IMPC).By providing raw data and the version of PhenStat used, resources like the IMPC give users the ability to replicate and explore results within their own computing environment.

View Article: PubMed Central - PubMed

Affiliation: The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

ABSTRACT
The lack of reproducibility with animal phenotyping experiments is a growing concern among the biomedical community. One contributing factor is the inadequate description of statistical analysis methods that prevents researchers from replicating results even when the original data are provided. Here we present PhenStat--a freely available R package that provides a variety of statistical methods for the identification of phenotypic associations. The methods have been developed for high throughput phenotyping pipelines implemented across various experimental designs with an emphasis on managing temporal variation. PhenStat is targeted to two user groups: small-scale users who wish to interact and test data from large resources and large-scale users who require an automated statistical analysis pipeline. The software provides guidance to the user for selecting appropriate analysis methods based on the dataset and is designed to allow for additions and modifications as needed. The package was tested on mouse and rat data and is used by the International Mouse Phenotyping Consortium (IMPC). By providing raw data and the version of PhenStat used, resources like the IMPC give users the ability to replicate and explore results within their own computing environment.

No MeSH data available.


Related in: MedlinePlus