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MOTIVATION Microarray experiments are affected by numerous sources of non-biological variation that contribute systematic bias to the resulting data. In a dual-label (two-color) cDNA or long-oligonucleotide microarray, these systematic biases are often manifested as an imbalance of measured fluorescent intensities corresponding to Sample A versus those(More)
OBJECTIVES To characterize second and third trimester fetal growth using Individualized Growth Assessment methods in a larger cohort of fetuses with normal neonatal growth outcomes. METHODS A prospective longitudinal study of 119 pregnancies was performed from 18 weeks, MA, to delivery. Measurements of several 1D and 3D fetal size parameters were obtained(More)
1 Overview The nnNorm package provides utilities to detect and correct for spatial bias with two color DNA microarrays (or paired single channel data). The normalization implemented in nnNorm package is based on neural networks models. Functionality to compare the distributions of the normalized log ratios is also provided. For the simpler case when only(More)
OBJECTIVE To compare third-trimester size trajectory prediction errors (average transformed percent deviations) for three individualized fetal growth assessment methods. METHODS This study utilized longitudinal measurements of nine directly measured size parameters in 118 fetuses with normal neonatal growth outcomes. Expected value (EV) function(More)
1 Overview This package implements the classification pipeline of the best overall team (Team221) (see Tarca et al. (2013a)) in the IMPROVER Diagnostic Signature Challenge described in Meyer et al. (2012). Additional capability is added to explore other combinations of methods for data preprocessing, feature ranking and classification described in Tarca et(More)
OBJECTIVE To evaluate the intermediate intracardiac diastolic velocities in fetuses with growth restriction. METHODS Doppler waveforms of the two atrioventricular valves were obtained. Peak velocities of the E (early) and A (atrial) components, and the lowest intermediate velocity (IDV) between them, were measured in 400 normally grown and in 100(More)
OBJECTIVES To assess the value of single and serial fetal biometry for the prediction of small- (SGA) and large-for-gestational-age (LGA) neonates delivered preterm or at term. METHODS A cohort study of 3,971 women with singleton pregnancies was conducted from the first trimester until delivery with 3,440 pregnancies (17,334 scans) meeting the following(More)
OBJECTIVE To evaluate the impact of late 3rd trimester fetal growth cessation on anatomical birth characteristic predictions used in classifying SGA neonates. METHODS A prospective longitudinal study was performed in 119 pregnancies with normal neonatal growth outcomes. Seven biometric parameters were measured at 3-4 weeks intervals using 3D(More)
1 Overview This package implements the Pathway Analysis with Down-weighting of Overlapping Genes (PAD-OG) algorithm described in Tarca et al. (2012). The method can be applied to analyze any type of gene sets yet in here it is illustarted using KEGG pathways. The method computes a gene set score as the mean of absolute values of weighted moderated gene(More)
OBJECTIVE To define modified Prenatal Growth Assessment Scores (mPGAS) for single and composite biometric parameters and determine their reference ranges in normal fetuses. METHODS Nine anatomical parameters (ap) were measured and the weight estimated (EWTa, EWTb) in a longitudinal study of 119 fetuses with normal neonatal growth outcomes. Expected third(More)
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