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Samples with parameters not meeting the above criteria were automatically regarded as samples from patients with pathological CSF findings.
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Firstly, with regard to each sample size, the sample with parameters most similar to the theoretical values is picked out from the formerly produced 1,000 Monte Carlo samples as the test sample for this sample size.
RSEM (v1.1.11) [ 27] was used to quantify transcript abundance in each sample, with parameters "--phred64-quals --fragment-length-minc-ci --outhenm --fragmentheength-min 100 --fRSEM-estimated-max 350", and then the RSEM-estimated fragment counts were fed into DESeq package (1.0.6) [ 28] to get the 'baseMean' value.
Small samples along with parameters close to the boundary may result in extra uncertainty in parameters and failure of the asymptotic assumptions, which are critical in maximum likelihood estimation.
In order to estimate the statistical scatter of these estimates, we simulated our whole procedure of estimation N b = 100 times on artificial GPD samples with known parameters.
Samples with acceptable parameters of RNA quality (Text S1) were hybridized to the corresponding Affymetrix oligonucleotide arrays, which were then scanned and expression data extracted using the standard Affymetrix Microarray Suite Software.
Spermograms were performed by experienced technicians and only samples with normal parameters were used (World Health Organization, 1999).
Spermograms were performed by experienced technicians and only samples with normal parameters were used [ 76].
In addition, we correlated the PRLR expression in tissue samples with clinicopathological parameters and disease-free and overall survival data.
Ensemble modeling proved to be a feasible method to separate samples with flux parameters that could be estimated from samples with poor information on the fluxes in the system.
For cDNA microarray data analyses, the significantly modulated genes were tested using Welch's t-tests between test and control samples with test parameter non-adjusted p < 0.05.
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