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Gene expression measures the genes that are being expressed on a given day.
Methodology included gene expression measures from microarrays, Gene Score Resampling for global ontological profiling, and semi-quantitative RT-PCR.
itPLIER normalisation and generation of gene expression measures was performed in GeneSpring GX 10.0 (Agilent Technologies, Inc .. Gene networks affected by anti-ANXA10 siRNA transfection were analysed by IPA software (Ingenuity Systems, Inc., Redwood City, CA, USA).
As a negative control, we applied csSAM to the simulated dataset of random gene expression measures and did not observe any cell-type-specific differentially expressed genes (Supplementary Fig. 2).
The goal of low-level analysis is to take raw data from the scanner, without any biological interpretation, and process it to produce cleaner and more meaningful gene expression measures.
To calculate gene expression measures, the data sets were normalized as follows.
Present call information from the MAS5.0 algorithm was added to the gcRMA gene expression measures.
We tested the hypothesis that deep sleep and gene expression measures taken from parietal cortex would correlate.
The spot mean signal intensities for probes passing the filter were quantile normalized [31] to generate gene expression measures.
We found inter-dependencies between the different sequences, and between the gene expression measures (Figure 2 and 3).
To calculate gene expression measures, the preprocessing method GCRMA was used [32], which is implemented in the package 'gcrma' of bioconductor (www.bioconductor.org).
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