my lab had an Affymetrix microarry done for some samples last year. What we got from the company that did them was an exel file with the differentialy expressed genes, the CEL files, jpg of the CEL files and a .DTT file under the header Raw Data.
The acompaning report said the DTT could be used in a command console? Does that mean R/bioconductor?
Or what can I do with that file ?
(note: we had 6 samples and got only one DTT file)
The raw data of your experiment is represented in the CEL files. These can be used for analysis in Bioconductor, or other tools.
The DTT file is an archive that can be created by several software tools from Affymetrix, such as the Command Console Software (AGCC), GeneChip Operating Software (GCOS) or Data Transfer Tool (DTT). The DTT archive contains the raw data files (CEL), plus some additional files (I believe the washing and staining protocols, library files etc). Since you can use the AGCC software (in stand-alone modus) for analyses as well, in addition to controlling the scanner, this will allow you to (re)do the analysis.
