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| Content Provider | Springer Nature : BioMed Central |
|---|---|
| Author | Heider, Andreas Alt, Rüdiger |
| Abstract | Background Microarrays have become a routine tool to address diverse biological questions. Therefore, different types and generations of microarrays have been produced by several manufacturers over time. Likewise, the diversity of raw data deposited in public databases such as NCBI GEO or EBI ArrayExpress has grown enormously. This has resulted in databases currently containing several hundred thousand microarray samples clustered by different species, manufacturers and chip generations. While one of the original goals of these databases was to make the data available to other researchers for independent analysis and, where appropriate, integration with their own data, current software implementations could not provide that feature. Only those data sets generated on the same chip platform can be readily combined and even here there are batch effects to be taken care of. A straightforward approach to deal with multiple chip types and batch effects has been missing. The software presented here was designed to solve both of these problems in a convenient and user friendly way. Results The virtualArray software package can combine raw data sets using almost any chip types based on current annotations from NCBI GEO or Bioconductor. After establishing congruent annotations for the raw data, virtualArray can then directly employ one of seven implemented methods to adjust for batch effects in the data resulting from differences between the chip types used. Both steps can be tuned to the preferences of the user. When the run is finished, the whole dataset is presented as a conventional Bioconductor “ExpressionSet” object, which can be used as input to other Bioconductor packages. Conclusions Using this software package, researchers can easily integrate their own microarray data with data from public repositories or other sources that are based on different microarray chip types. Using the default approach a robust and up-to-date batch effect correction technique is applied to the data. |
| Related Links | https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-75.pdf |
| Ending Page | 10 |
| Page Count | 10 |
| Starting Page | 1 |
| File Format | HTM / HTML |
| ISSN | 14712105 |
| DOI | 10.1186/1471-2105-14-75 |
| Journal | BMC Bioinformatics |
| Issue Number | 1 |
| Volume Number | 14 |
| Language | English |
| Publisher | BioMed Central |
| Publisher Date | 2013-03-02 |
| Access Restriction | Open |
| Subject Keyword | Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms iPSC Microarray Platform Batch Effect NCBI Gene Expression Omnibus Chip Type Computational Biology/Bioinformatics |
| Content Type | Text |
| Resource Type | Article |
| Subject | Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology |
| Journal Impact Factor | 2.9/2023 |
| 5-Year Journal Impact Factor | 3.6/2023 |
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