Data Extraction
NimbleGen arrays are scanned on a 5-micron scanning platform, where the image is saved as a standard TIFF file. Roche NimbleGen has developed a proprietary software package, NimbleScan, for automated image extraction and analysis, which we use on all assays performed by our service facility. This application accepts an image file and an array description file, automatically locates the feature grid within the array, quantifies the individual features, and generates a feature report in the appropriate format for the data analysis requirements of a specific application.

Data Analysis
Depending on the array application, a range of data analyses are performed to simplify the interpretation large data sets. For genomic DNA-targeted array experiments, the data sets are delivered as GFF files allowing visualization in SignalMap, Roche NimbleGen's data browser software. For each array application, Roche NimbleGen provides the following data formats, along with the raw data files:

• DNA Methylation
  Scaled log₂-ratio data GFF file (ratio of control vs. sample for individual probes)
  Genome annotation GFF file (primary transcript, tiled regions, CpG islands)
  P-value GFF file (positive enrichment score for individual probes)
  Peaks GFF file (regions of significant enrichment)
  Summary reports (maps peaks to the transcription start site of a gene)
• CGH
  Segmentation analysis using NimbleGen's segMNT v1.1 algorithm
  Segmentation GFF files
  Segmentation PDF files
  Segmentation TXT files
  Genome Annotation GFF files
• ChIP-chip
  Scaled log₂-ratio data GFF file (ratio of control vs. sample for individual probes)
  Genome annotation GFF file (primary transcript and tiled regions)
  Peaks GFF file (regions of significant enrichment)
  Promoter reports (maps peaks to the transcription start site of a gene)
• Gene Expression
  Normalized gene calls using the RMA package
  Array images
  Microarray design files
  Gene descriptions
  Probe and gene sequences
• Comparative Genome Sequencing
  Genome Annotation
  Categorized SNPs
  Uncalled Differences
  Resequenced Regions
  Average Ratio

Roche NimbleGen data sets can be used with a number of commercial and freely distributed microarray expression packages including the R statistical package and SpotFire Decision Site.