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FlyChip
Functional Genomics for Drosophila
Cambridge Systems Biology Centre, Tennis Court Road, Cambridge, CB2 1QR, UK  [map]
Tel: +44 (0)1223-760280.   Fax: +44 (0)1223-760241.

Analysis

Non-technical description of how we analyse each spotted microarray experiment (gene expression arrays)

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.