The workbench assumes that expression values are given at the gene level, thus probe-level analysis of e.g. Affymetrix GeneChips and import of Affymetrix CEL and CDF files is currently not supported. However, the workbench allows import of txt files exported from R containing processed Affymetrix CEL-file data (see Affymetrix GeneChip).
Affymetrix NetAffx annotation files for expression GeneChips in csv format and Illumina annotation files can also be imported. Also, you may import your own annotation data in tabular format see Generic expression and annotation data file formats).
Below you find descriptions of the microarray data formats that are supported by CLC Main Workbench. Note that we for some platforms support both expression data and annotation data.
- GEO (Gene Expression Omnibus)
- Affymetrix GeneChip
- Illumina BeadChip
- Gene ontology annotation files
- Generic expression and annotation data file formats