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The answers obtained from both samples were combined for our analyses.
Paired end reads for both samples were combined and mapped to the reference human genome (UCSC hg19) using BFAST (http://bfast.sourceforge.net) [ 11].
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The mapped 454 reads from both population samples were combined and aligned against the masked, annotated reftigs with mpileup of SAMtools [ 33].
Both within-patch samples were combined and sealed in plastic bags and transferred to 90% ethanol solution for storage.
If fluid was obtained from either one or both breasts, all samples were combined into a single sample preservative vial.
Furthermore, when both of these samples were combined, prediction relying on monocyte IL-6 secretion was similar to this study (manuscript in preparation).
By univariate and multivariable analysis, a lower DR5 WI was significantly associated with smokers compared to non-smokers when both groups of tumor samples were combined (i.e., Tu−Met and Tu+Met) (P<0.05).
However, it is likely that selection on this locus is not connected to migration because, first, there was no such peak in the FST analysis, and second, both resident and migrant samples were combined for the Little Sheep Creek Tajima's D analysis.
Two cohorts of the top one-third TBX3 and TBX2 expressing samples were combined and duplicates samples were removed.
Four samples were combined in a single deep sequencing lane, and barcode sequencing was performed.
The two samples were combined and weighted together (more details are here).
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