Sentence examples for used the default method from inspiring English sources

The energy minimization used the default method of AMBER 5.0 (10 cycles of the steepest descent method followed by the conjugate gradient method).

For these two types of analysis we used the default methods for calculating the F statistic, AI optimisation and a maximum of 20 iterations.

The nuclear size was calculated at each time point using the default method of ImageJ based on IsoData algorithm.

Additionally, model performance was also evaluated using the default method of determining the area under the receiver operating characteristic curve (ROC) for the Maxent model.

The genes and experiments were median centered and normalized using the default method for this software.

The chip signals were normalized using the default method in Affymetrix MAS5, but setting the target at 2%-trimmed mean to 1500 instead of 500.

RNA-seq counts were normalized with DESeq (Anders and Huber 2010) using the default method, as described in Swart et al. (2013).

Two-channel normalization was performed to adjust the centre and spread of the distribution of intensity log-ratios [ 61] using the default method of the "marray" package [ 62] in Bioconductor version 1.8 [ 63].

Following the procedures described in the edgeR documentation, read count tables were loaded into R, normalized using the default method for edgeR (trimmed mean of M values, or TMM), and then tested for differential expression using the exactTest method.

These valences were satisfied by using the default method of capping them with a hydrogen atom in the direction of the connecting atom in the medium level with a C H distance of 0.723886 times the C C distance.

The five calibration approaches were individually validated using the "default" method for each [i.e., spiking blank plasma samples (or sample digest) with the corresponding calibrators (peptides, extended-peptides or protein) of each calibration approach].