Microarray Quality Check
Load Data file
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Select type of file

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Load Setup file
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Quality check method
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Email (Optional)
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Run

Input Data

To load a set of CEL files as raw data they should be compressed in a .zip archive with a name without spaces. It is also possible to load already normalized data in a text file, in which the first column should be the probeset IDs and subsequent columns contain the normalized data for each sample. The first line is a header with the sample names (also used in the setup-file). Avoid using sample names starting with numbers. See the example files under General instructions.

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Contact

Enter your E-mail Id for getting the result in your mail.

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Input Setup

The setup file should describe the experimental setup assigning each sample to a specific condition. The format of the file should be as follows: The first column should contain the names of the CEL files (or the sample names used in the header of the normalized data file) and additional columns should assign attributes in some category to each array. See the example files under General instructions.

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Microarray Quality Check

Raw or pre-normalized microarray data are subjected to the classical preprocesing steps (normalization, probe set summarization). A number of quality controls are then run on the preprocessed data in order to identified potential erronous arrays that may be removed before subsequent downstream analysis.

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General Instructions

Click [?] to display instructions here, or navigate through the links below.

Tool description
Input instructions
Output description

Example files to download

Normalized data
Raw data
setup file

Click load Example file and hit Run

Input Instructions

Either raw CEL files (as a .zip archive) or prenormalized data can be used as input. A setup file is also needed to assign the samples into conditions or groups.

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Output file description

Each quality control method will generate one or several figures which can be viewed and downloaded or emailed to the supplied address.

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Quality check methods

Select the quality checks that you wish to perform.

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Citations
1) Väremo L, Nielsen J, Nookaew I ( 2013) Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods Nucleic Acids Res. Apr;41(8):4378-91
A * indicates that these authors contributed equally to the work.