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EEM: Extraction of Expression Modules

Extraction of Expression Modules. Breast tumor microarray data. Preprocess the expression file. Convert probe IDs to gene symbols. The CHIP file format contains annotation information about a microarray. It lists the features (i.e probe sets) used in the microarray along with their mapping to gene symbols (when available). More information about the CHIP file format can be found here. Convert Expression Value to the log-scale. Number of genes after variation filter.

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Extraction of Expression Modules. Breast tumor microarray data. Preprocess the expression file. Convert probe IDs to gene symbols. The CHIP file format contains annotation information about a microarray. It lists the features (i.e probe sets) used in the microarray along with their mapping to gene symbols (when available). More information about the CHIP file format can be found here. Convert Expression Value to the log-scale. Number of genes after variation filter.

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Extraction of Expression Modules. Breast tumor microarray data. Preprocess the expression file. Convert probe IDs to gene symbols. The CHIP file format contains annotation information about a microarray. It lists the features (i.e probe sets) used in the microarray along with their mapping to gene symbols (when available). More information about the CHIP file format can be found here. Convert Expression Value to the log-scale. Number of genes after variation filter.

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EEM: Extraction of Expression Modules

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Extraction of Expression Modules. FAQ - Frequently Asked Questions. How long do you keep the result files? 2 weeks. Please download and save your result. If you provided us with an email, we will send you a message announcing the impeding deletion of your results files. This should give you enough time to download your data. Your email will also be deleted after 2 weeks and NEVER be passed on to others. What are the file-size limits? 64MB is the maximum size for the expression and geneset files.

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EEM: Extraction of Expression Modules

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Extraction of Expression Modules. Preparing Files for EEM. Before using EEM, please prepare the following two files:. This file includes features (genes or probes), samples, and an expression value for each feature in each sample. The two file formats are available: GCT, Gene Cluster Text file format (*.gct), and TXT, Text file format for expression dataset (*.txt), which are supported in GSEA. For descriptions and examples of each file format, please have a look at the GSEA file formats. If you want to ...

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EEM: Extraction of Expression Modules

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Extraction of Expression Modules. Model-free unsupervised gene set screening based on information enrichment in expression profiles. Niida A, Imoto S, Yamaguchi R, Nagasaki M, Fujita A, Shimamura T, Miyano S. Bioinformatics. 2010 Dec 15;26(24):3090-7. Epub 2010 Oct 19. Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. Niida A, Imoto S, Yamaguchi R, Nagasaki M, Miyano S. PLoS One. 2010 Jun 9;5(6):e10910.

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XiP (eXtensible integrative Pipeline) is a flexible, editable and modular environment with a user-friendly interface that does not require previous advanced programming skills to run, construct and edit workflows. XiP allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed. SiGN-SSM is software for estimating dyna...

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EEM: Extraction of Expression Modules

Extraction of Expression Modules. Breast tumor microarray data. Preprocess the expression file. Convert probe IDs to gene symbols. The CHIP file format contains annotation information about a microarray. It lists the features (i.e probe sets) used in the microarray along with their mapping to gene symbols (when available). More information about the CHIP file format can be found here. Convert Expression Value to the log-scale. Number of genes after variation filter.

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