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This bias increases when the shift size increases since a very short run of samples coming from the out-of-control state of the process with a high variance was used.
This is due to the early detection of such shifts by the c-chart that leads to a very short run of samples after the change which then compresses the data and hence informs the MCMC algorithm.
Red bars indicate reads from Miseq run of samples normalised using the Sequalprep (Invitrogen) plate-based normalisation kit.
Each run of samples included negative controls (no PCR template) and positive controls (HPV plasmid in low copy number).
These can then be averaged over the complete run of samples to provide an overall confidence that this particular formula is present in the data.
The detection limit for mercury and selenium was 0.5 nmol/L and 0.1 μmol/L respectively, and each run of samples included a standard.
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All of the detected PIK3CA mutations were confirmed in the second independent run of sample testing.
All detected mutations were confirmed in the second independent run of sample testing.
We calculated the costs for all materials and reagents including those associated with the running of samples on the ABI 3130 XL sequencer.
Before spiking, the actual cell number of HCC1937 cell line was determined using BD TruCount tubes (BD Biosciences, San Jose, CA, USA), containing a known number of fluorescent beads and by running of samples on a flow cytometer (FACS Calibur, BD Biosciences, San Jose, CA).
Quality assessment of samples confirmed 3′-end/-middle (3′/M) ratios for housekeeping genes below the required threshold of 3, which confirms linear amplification of samples before running of samples and was in keeping with the high-quality threshold set for the samples utilised (Supplementary Figure S3).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com