GENOMESTUDIO USER GUIDE PDF
This download contains the user guides for GenomeStudio Software GenomeStudio Genotyping Module v User Guide. Notice. This publication and its contents are proprietary to Illumina, Inc., and are intended solely for the. GenomeStudio Gene Expression Module v User Guide. Notice. This publication and its contents are proprietary to Illumina, Inc., and are intended solely for.
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Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina guied arrays for a broad user community, we have developed a module for ArrayAnalysis.
This module can be used together with existing modules for statistical and pathway analysis to provide a genomesrudio workflow for Illumina gene expression data analysis. The outputs are directly linked to the existing statistics module of ArrayAnalysis.
The Illumina bead arrays analysis module is available at uuser A user guide, a tutorial demonstrating the analysis of an example dataset, guode R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life guidw research. The online version of this article doi: Illumina bead arrays [ 1 ] are a popular choice for array-based genome profiling studies.
Although Next Generation Sequencing technology is on the rise, microarray-based gene expression profiling is still widely utilized due to its ease of use, robust performance, reproducibility, and low per-sample cost. Furthermore, open data repositories e. ArrayExpress [ 2 ] and Gene Expression Omnibus [ 3 ] contain a vast amount of microarray experiments, which are often re-analyzed, integrated, or combined with newly generated data in the context of modern integrated systems biology research.
This process is facilitated by easy access to streamlined processing. To extract biologically meaningful information from genome profiling experiments, generated data first needs to be quality checked, filtered, pre-processed and statistically analyzed. As gene expression profiling experiments are typically designed, performed, and interpreted by biological domain experts rather than bioinformaticians, it is important to enable these researchers to independently operate basic analysis pipelines.
Pipelines with a user interface that provides immediate and intuitive feedback are of great interest for increasing efficiency and effectiveness of the research process. Besides proprietary vendor-provided software BeadStudio, GenomeStudio and open-source software Illuminaio [ 4 ], several pre-processing and quality control QC methods for Illumina bead arrays are available beadarray [ 5 ]; lumi [ 6 ]; limma [ 7 ]. However, utilization of these methods requires extensive bioinformatics skills and therefore they are not readily accessible for a broad researchers community.
To extend utility of analysis workflows for Illumina bead arrays also to non-bioinformaticians, we have created an open-source, user-friendly workflow, accessible via the web interface of ArrayAnalysis.
The relevance of analysis workflows for Illumina bead arrays that are friendly to a wide range of researchers has been recognized by several other bioinformatics developers, resulting in availability of tools and pipelines related to our work e.
Nevertheless, our module for ArrayAnalysis. For instance, Chipster provides similar functionality but requires local software installation and availability of specific Java versions; Madmax is not open source and requires login credentials to be provided by the developers; and IlluminaGUI requires a local install of R and its support has been discontinued. Therefore, our web interface-based workflow is a convenient resource for free, fast and user-friendly analysis of Illumina bead arrays by a broad community of researches – regardless of their bioinformatics skill level or research budget.
The Illumina QC and pre-processing module was developed to complement and link to previously created modules for analysis of microarrays, available at www.
The Illumina module has been implemented as a wizard guiding the users through the different steps and is connected in an ArrayAnalysis workflow to downstream modules for statistics and pathway analysis. Schematic representation of the different steps in the data workflow for Illumina bead arrays.
Steps 1—5 are part of the newly added Illumina QC and pre-processing module. Illustrative examples of such tables and images are shown array boxplots, array correlation heatmap, head of normalized data table. Optionally, steps 1 to 5 of the pre-processing procedure may be repeated after exclusion of low quality arrays. The output files can be further used to perform statistical analyses through the statistics module and pathway analysis through the pathway analysis module, or to proceed with downstream analyses in external tools.
The module was implemented using R and Bioconductor packages for Illumina analysis lumi [ 6 ] and limma [ 7 ] to provide the user with the most commonly used analysis options. Using the lumi package, we implemented various types of background correction e.
Additionally, the neqc method from the limma package has been included, which performs a background correction using a normal-exponential-modeling approach [ 12 ] followed by uaer quantile normalization of all regular and control probes together, and a log2-transformation on the dataset. After normalization, probes with intensities below detection level can be removed to speed up the processing and to reduce false positives.
Five types of quality control QC plots are implemented: All plots use consistent colors for arrays and experimental groups and can jser generated for both raw and pre-processed data, which helps to assess whether the pre-processing step corrects possible aberrations. The Illumina identifiers are converted to equivalent nucleotide universal identifiers nuIDs [ 13 ] based on their probe guuide. After quality control and pre-processing, the nuIDs are used to add additional annotation e. When running the Illumina workflow, the user is guided through the different analysis guidde via a web based user interface.
The user may choose to perform all pre-processing steps within our workflow recommendedor to provide already background-subtracted data.
Both summarized probe-level and summarized gene-level input data are supported.
GenomeStudio Software 2011.1 User Guides
Summarized probe-level data is recommended as input, as genomestjdio will eliminate the occurrence of improper combinations of the expression values of different probes into a single-gene value [ 14 ].
In the second step, the user can annotate the imported samples by entering custom sample names and experimental group names by either uploading a sample description file or entering the sample description information manually via the web based interface.
Genomsstudio third step summarizes the information about the uploaded data and provides the user with the option to henomestudio an email address for notification when the workflow has finished. This encompasses the removal of per-array technical effects, which ensures that the values being further analyzed reflect underlying biology. Three actions are typically performed to achieve the following [ 14 ]: The user may choose between two popular pre-processing approaches that implement these actions for Illumina venomestudio Also, the user can choose the types of plots that are to be created and whether filtering probes with intensities below detection guids is to be performed.
Upon completion of the run, the user receives a link to download a zip archive of results either at the web-interface or by email. If the QC diagnostic plots show arrays of insufficient quality, the pre-processing procedure may be repeated after exclusion of those gehomestudio. Otherwise, the user can immediately proceed with the next module of the workflow to perform statistical analysis.
Via a web interface, the existing statistics module prompts the user to specify which experimental groups are to be compared e. After submitting the choices, this module runs limma model fitting to compute a table of relevant statistics, including estimated coefficients effect sizes and their significances [ 7 ]. Results from the statistics module genkmestudio then be used for further pathway suer processing in a downstream module that makes automated calls to PathVisio [ 15 ] or they can be downloaded for processing in other software.
Running time of an analysis is very much dependent on the size of the input file, the number of arrays, the specific user settings, and the modules used, and will genomeestudio from minutes to hours in the extremes. Performance of ArrayAnalysis servers is being monitored to make sure they effectively deal with the workload, and extra capacity can be allocated in future if needed. When not surpassing a dozen concurrent runs, running times will not increase much. Additionally, users can download the R scripts to run on their own systems if desired, for example in case of many projected runs or very large data sets that would not be convenient to process over the internet.
The scripts have been designed for ease-of-use, providing a separate initiation script to specify user settings e.
The addition of the currently introduced Illumina module complements ArrayAnalysis.
It provides users of this platform or those processing existing data not only with an easy to use data quality control and pre-processing web module, but also with a direct connection to further modules offering downstream statistical and pathway analysis functionalities. As genokestudio whole, ArrayAnalysis. Being an open source project, developers within the user community can contribute by adding modules or improving functionality of existing ones, and source code can be downloaded for local deployment.
The developed Illumina bead array analysis workflow provides an easy, fast, and intuitive way for quality control, pre-processing, statistical, and pathway analysis of Illumina gene expression arrays for a broad range of researchers. The workflow provides immediate feedback on quality and basic statistics outcomes of generated data, increasing the speed and iterative capacity genomwstudio intuitive research pipelines.
Genomedtudio enables researchers to effectively resolve the first steps in data analysis and focus on their primary interest: The workflow can therefore be used as a starting point facilitating a broad range of applications in life sciences research. All authors received the funding for this research and preparation of the manuscript from respective institutes they are affiliated with: Funding bodies did not have any role in study design, collection, analysis and interpretation of data, in the writing of the manuscript, and in the decision to submit the manuscript for publication.
We thank Nuno Nunes for technical support and system maintenance of the ArrayAnalysis. No materials were used in this study. Authors have obtained permission from all those mentioned in the Acknowledgements. The Additional files are given for reference, most recent versions are available from http: Tutorial demonstrating analysis of a publicly available example dataset from ArrayExpress.
MR, CE, conceived the research. All authors read and approved the final manuscript. National Center for Biotechnology InformationU. Published online Jun EijssenVarshna S.
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GoelelaThomas KelderMichiel E. AdriaensChris T. Eveloand Marijana Radonjic. Author information Article notes Copyright and License information Disclaimer. Received Jan 5; Accepted Jun 5.
This article has been cited by other articles in PMC.
GenomeStudio User Guides
Abstract Background Illumina genomsetudio expression bead arrays are a widely used platform for transcriptomics. Results To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.
Conclusions The Illumina bead arrays analysis module is available at http: Electronic supplementary material The online version of this article doi: Background Illumina bead arrays [ 1 ] are a popular choice for array-based genome profiling studies.
Implementation The Illumina QC and pre-processing module was developed to complement and link to previously created modules for analysis of microarrays, available at www. Open in a separate window.
Results and discussion When running the Illumina workflow, the user is guided through the different analysis steps via a web based user interface. Conclusions The developed Illumina bead array analysis workflow provides an easy, fast, and intuitive way for quality control, pre-processing, statistical, and pathway analysis of Illumina gene expression arrays for a broad range of researchers.
Availability and requirements Project name: Acknowledgements All authors received the funding for this research and preparation of the manuscript from respective institutes they are affiliated with: Additional files The Additional files are given for reference, most recent versions are available from http: