Alternatively, we only conducted the baseline correction, normalization and smoothing for the HCC, prostate, and cirrhotic data, where the smoothing method was selected as the ' least-square polynomial' smoothing instead of the ' lowess' smoothing.
Alternatively, we only conducted the baseline correction, normalization and smoothing for the HCC and Cirrhosis, HCC and ToxPath data (The smoothing method is selected as a different ' least-square polynomial' algorithm) [ 25, 26].
In case an association analysis using DNA pools in both groups is to be conducted, the k-correction seems to be a slightly more precise method (if corrections values of heterozygous SNP calls are available) than using uncorrected RAS values obtained from the Birdseed2 calling algorithm being the second best option.
To reduce the type I error, we conducted the Benjamini-Hochberg correction for multiple testings [ 17].
We conducted the multiple testing correction using the Benjamini Hochberg procedure (Benjamini and Hochberg 1995) at a 5% of false discovery rate (FDR), which was implemented in the multtest package of the R programming language.
To achieve this, all searches were conducted using the correction for PSI-BLAST-statistics based on sequence composition [ 38] and the e-value threshold for inclusion in the profile was set at.001.
Care was, therefore, exercised to narrow the frequency ranges of Raman spectra to within those of particular interest when conducting the background correction.
The proposed method, in contrast to standard CT, allows the appreciation of the revealed changes, to diagnose the early symptoms of ARDS on the first day, to analyze the development of pathologic in dynamics and to conduct the treatment correction in time.
Since both the over-representation analysis and the gene set enrichment analysis were applied to many GO categories, we further conducted the false discovery rate (FDR) correction, which provides strong control to have less false negatives at the cost of a few more false positives.
