Mark J Dunning, Nuno L Barbosa-Morais, Andy G Lynch, Simon Tavaré, Matthew E Ritchie
The ftp site the raw data were hosted on is currently down. An alternative location will be provided shortly.
Bead level data
- Image plots of foreground intensities for each strip on each BeadChip (log-2 transformed)
- Image plots of background intensities for each strip on each BeadChip (log-2 transformed)
- Boxplots of foreground intensities (background subtracted, log-2 transformed and colour coded by BeadChip)
- Boxplots of background intensities (log-2 transformed and colour coded by BeadChip)
Bead summary data
- Smoothed scatter plots of summarised intensities (log-2) of individual arrays against median array
- Boxplots of summarised intensities per array (colour coded by BeadChip, non-normalised)
- Boxplots of standard errors per array (colour coded by BeadChip, non-normalised)
- Boxplots of number of beads per bead type per array (colour coded by BeadChip, non-normalised)
- Number of false discoveries versus number of genes selected for each contrast. Bead types were ranked using log-odds.
- Targets file Text file listing all array names and spike concentrations
- Results of the re-annotation for all non-spikes and non-controls
- Intensities of each control probe on every array as exported by BeadStudio
- Averaged control profile as exported from BeadStudio
- Sequences for the Illumina controls used in the experiment
- Pre-calculated thermodynamic values for each spike probe
- File giving bead IDs, targets and sequences for the spikes
- Bead summary data .rda (sharpened, locally background corrected, summarised)
- BeadStudio output (non-normalised). The file SampleProbeProfile.txt contains summary data for the non-spikes. The file ControlProbeProfile.txt contains summary data for the spikes and other control probes. The spikes have 'DRC' as their TargetIDs.
We are grateful to Illumina for allowing us to make this data set publicly available. In particular, we thank Gary Nunn and Semyon Kruglyak for retrieving these data for us.
- Full Analysis Script R code to read the bead level data above and re-produce all the figures and numerical values quoted in the paper. Note that reading the bead level data requires around 4Gb of RAM.