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This finding was replicated even when we only probed the maximally activated voxel of individually defined ROIs, suggesting that these results are not due to low sensitivity of the group-averaged ROI analysis.
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Then we clustered probes with genomic distance <30 Kb, and <span class="lh">we considered only probes belonging to at least a 2-probe cluster.
For each probe set, we compute a ratio of the variance of the expression levels between replicates to the expression variance between cell lines, and we keep only probe sets for which this ratio is sufficiently low; the threshold we use is the first quartile of this ratio among all probe sets.
It should be noted that we selected only probes scored as "present call" in all samples, which allows relatively accurate comparison of expression levels between samples.
For this analysis, we included only probe sets detected at p<0.05 in at least two individuals among the mice involved (i.e. the cafeteria, fast food and chimpanzee diets).
We considered only probe sets that were present in both array types U133a and U133plus2.
We used only probe sets that mapped unambiguously to Ensembl gene IDs with KEGG annotations [ 22].
We kept only probe sets which matched to a unique Ensembl gene.
In the analysis of the exon array data, we included only probe sets derived from the core set.
Clustering of Probes and Functional Predictions We analyzed only probes significantly regulated (|log2 fold-change)|log2 fold-change1) in end-stage M marinum samples (Dionne et al., 2006 ).
We analyzed only probes significantly regulated (|log2 fold-change)|log2 fold-change1) in end-stage M marinum samples (Dionne et al., 2006).
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