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Basic Plug-in is a package of statistical tools which are widely used for microarray data analysis.
Omics data analysis is not straightforward and is hard to establish a universal protocol. It’s very important to understand what you are actually doing in each step of analysis. The visual aid and intuitive interface of Basic Plug-in help your learning statistical concepts.
If you have no or little experience in the omics data analysis, we strongly recommend you purchase Initiation Service as well so that you can focus on biological discovery in a context of your study, which is the most important part.
See What You Can Do with Basic Plug-in:
- Normalization
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- Coordinate blocks to define normalization. You can promptly recall a saved normalization scheme.
- Filtering
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- You can filter out genes by flag or signal values to remove noise disturbing statistical analysis.
- Find Similar Pattern
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- You can extract genes which are correlated or anti-correlated to a template pattern.
- Differential Expression
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- You can extract DEG (Differentially Expressed Genes) by fold and/or p-value. P-values can be corrected by BH FDR.
- ANOVA
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- You can extract genes which are differentially expressed among groups by ANOVA.
- Clustering
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- Hierarchical clustering is useful to group genes and samples by gene expression profiles.
- PCA
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- PCA is useful to summarize expression profile, especially for researching pathology and diagnosis.
Function List:
- Normalization
- Arithmetic operations, log transformation, global normalization, quantile normalization, making ratios to average or control samples.
- Filtering
- Filtering by signal intensities, log ratios or flag values.
- Find Similar Pattern
- Filtering by correlation against an average pattern of selected genes.
- Differential Expression Analysis
- Fold differences, one-sample t-test, Student T-test, Welch T-test, Mann-Whitney U-test, BH FDR correction.
- ANOVA
- One-way ANOVA for multiple groups. BH FDR correction.
- Clustering
- Building a tree by average linkage (UPGMA). Similarity measure options are Pearson correlation, Standard correlation, Spearman rank correlation, Euclidean distance.
- PCA
- Visualizing component scores of samples. And you can export genes with loadings of any components.
Technical Support (Free):
Self-Support (Free):
Workflow with plug-ins:
