Microarray Data Analysis
Microarray experiments generate large amounts of data, which might be difficult for standalone computers to handle. In addition, the intricacies in data analysis leave users undecided on how to find a correct solution. We, at Ocimum, have a team of well-trained bioinformaticians and statisticians to handle such data. Our high-end servers help us in working with large microarray data in a fast and efficient manner.
Depending on your requirements you can choose from the following services:
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Basic Analysis
- Data preprocessing: Data preprocessing includes ratio calculation and outlier rectification followed by log transformation.
- Data normalization: We study your data and apply appropriate normalization techniques to bring the samples and genes to a common platform for better comparison.
- Handling missing values: Missing values or invalid values are substituted with appropriate values.
- Data filtration: Genes that are not affected by treatments are removed using the concept of fold change. Filtration is also done on calls in case of Affymetrix arrays.
- Handling replicates: Replicated genes and samples are handled and in the process, genes showing non-significant variation across samples are removed. ANOVA technique is used for this.
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Standard Analysis
- Includes all basic analyses.
- Clustering: K-means clustering and SOM clustering is performed on the filtered data. Significant clusters are further subjected to hierarchical clustering to find fine relationship among genes.
- Annotation: All genes present in clusters are annotated using our curated biological database.
- Gene ontology: Ontology analysis is performed on filtered genes and the functions significantly affected along with their genes are reported.
- Pathways: Pathways analysis is performed on filtered genes and the pathways significantly affected along with their genes are reported.
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Customized Analysis
- Customized analysis is performed as per user request.
- It can include large deviations from routine microarray analysis.
All analysis results are provided as graphs and tables in Excel and as a PDF document.
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