The first two principal components, which capture 82% of the variance (Figure S3), appear to be dominated by differences between sample groups while principal component 3 captures variation largely within sample groups.
The inclusion of variation caused by expression differences between samples used for protein and mRNA measurements means that we expect the actual correlation between protein and mRNA expression to be better than that observed.
Also, levels of differentiation do not seem to have been influenced by temporal differences between samples.
In doing so, we have pinpointed specific, differentially methylated CpG sequences that were highly informative between sample types and by individual differences between samples.
These discrepancies might be explained by differences between the two samples (chronological age and IQ scores) as well as in task design.
We also found that sample clustered largely by patient, with differences between samples from the same patient likely due to different time points of sample collection.
This is to avoid the potential bias caused by the conditional differences between samples, such as sequencing depth, library preparation errors, and so on.
A qRT-PCR reaction for the exogenous RCP1 control gene was performed to allow for standardization of expression of the CF genes by accounting for differences between samples in the RT reactions.
Equal amounts of protein are used for each sample under comparison so that any differences in relative peptide/protein amount measured by mass spectrometry reflect differences between samples, not starting protein amounts.
After the initial reductions between source and POU, we observed an increase in contamination in about half of the households, as can be observed in Figures 3 and 4 and as evidenced by differences between household and control samples (Tables 3 and 4).
