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Suppressing viral load could allow for variants within BM to replicate separately and appear as distinct from that in blood, while high viral loads in all tissues could cause a "swamping" of signal, in which plasma virus flooding the tissues obscures detection of within-tissue replication.
As a next step we therefore analyzed alterations in gene expression in each biological replicate separately.
Hence, samples with ≤1000x and >1000x were normalized by the sum of each replicate separately.
Reads uniquely aligned to each gene were tabulated from each replicate separately.
We calculated the expression level (RPM) for each replicate separately and compared them to one another.
B-score normalization was then applied to each replicate, separately, and included corrections for plates, rows and columns [ 10, 11].
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The assignment procedure is carried out country-by-country and replicated separately for literacy and numeracy.
Finally, we tested whether the observed correlation can be reproduced using the protein expression data from each of the two sets of experimental replicates separately.
For each probe that passed the p-value filter (n = 21178) the Pearson correlation coefficient between the log2 median centered intensities in the FFPE samples and in the FF counterparts (considering all replicates separately) was calculated.
Assay biological replicates separately.
Therefore, sex was included in the experimental design as an additional factor by running replicates separately for each sex.
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