Analysis
Non-technical description of how we analyse each spotted microarray experiment (gene expression arrays)
- See FCAN for an overview of our automated data analysis pipeline
- See scanning for a description of microarray image acquisition
- See spot signal for a description of how we find and then quantify the spot signals
- See assign ID for a description of how we assign the spot identities
- See normalise for a description of how we correct known sources of systematic bias
- See statistics for a description of our standard methods
- See data release for a list of the files that we will send to you
- See downloads for spot description and 'Affymetrix to FlyChip' mapping files, etc...
Non-technical description of how we analyse each Affymetrix microarray experiment
We provide the image (DAT) and raw intensity (CEL) files.
We use the standard tools available from Affymetrix to extract the raw signals from the images. For gene expression experiments, we recommend use of bioconductor packages. Normalisation and peak detection can be performed with TiMAT. We do not perform any downstream statistical analyses.
Non-technical description of how we analyse each Nimblegen microarray experiment
We provide the image (TIF) and raw intensity (PAIR) files.
We use NimbleScan to extract the raw signals from the images. For gene expression experiments, we recommend use of bioconductor packages. Normalisation and peak detection of ChIP or DamID experiments can be performed with MA2C. We do not perform any downstream statistical analyses.
Further help required...?
For a general introduction to the analysis of microarray experiments and links to useful tools, please refer to data analysis in links. Funding limitations mean that FlyChip is unable to provide comprehensive analytical support for end-users.
