Sentence examples similar to rma standard from inspiring English sources

NUSE is calculated by standardizing RMA-estimated standard errors across arrays.

RMA, a standard data analysis algorithm for calculation of expression estimates from Affymetrix GeneChips [ 17] was used initially for calculation of DNA copy number differences.

The summarization step estimating gene expression levels was slightly modified from standard RMA, not taking into account the chip-exon effect, that is, ruling out the relative change for the sample in a particular exon.

For the Affymetrix U133A and U133 Plus 2.0, we chose the fRMA (32) normalizing algorithm, a variant of the standard RMA (33) algorithm that uses publicly available microarray databases to estimate probe-specific effects and variances, instead of using only the samples from the data set to be normalized.

We also estimated the allometric coefficients using the reduced major axis (RMA) and calculated their standard error [32].

Separated gene expression analyses of these two datasets were performed using standard methods: RMA algorithm [45] was used to normalize data within each of the experiments.

We could not determine the effect of H60a elongation on the NK-cell cytokine response, because there was no IFN-γ secretion in response to the RMA cells expressing the standard form of H60a (data not shown), possibly reflecting relatively low levels of H60a cell surface expression.

When CD45−/− NK cells were used as effectors in killing assays with RMA cells expressing the standard or elongated H60a molecules as the targets, we observed that elongation of H60a reduced lysis by these NK cells in the same manner as for CD45 positive WT NK cells (Fig. 5), demonstrating that the effects of ligand elongation were not solely caused by reduced segregation of CD45 from NKG2D.

Data were pre-processed using the GC-Robust Multi-array Average (GC-RMA) procedure, Normalized Unscaled Standard Error (NUSE) and Relative Log Expression (RLE) measures were calculated to verify the technical homogeneity of the dataset.

The rma algorithm differs from the standard Affymetrix algorithm in a number of ways; most importantly, the data are quantile quantile normalised at the probe level, prior to calculation of a final expression summary from the positive match (or PM) probes alone.

Signals were log transformed and standardized to a mean of 8 and a standard deviation of 2. RMA normalization was also applied to the lung data (Affymetrix M430v2).