Technical variation plays an important role in microarray-based gene expression studies, and batch effects explain a large proportion of this noise. batch effects between replicates. In a second step, quantile normalization prior to batch effect correction was performed for each method. Technical variation between batches was evaluated by principal component analysis. Associations between body mass index and transcriptomes were calculated before and after batch removal. Results from association analyses were compared to evaluate maintenance of biological variability. Quantile normalization, separately performed in each batch, combined with successfully reduced batch effects and maintained biological variability. performed perfectly in the replicate data subset of the study, but failed when applied to all samples. All other methods did not substantially reduce batch effects in the replicate data subset. Quantile normalization plus appears to be a valuable approach for batch correction in longitudinal gene expression data. Introduction Gene expression profiles measured by microarrays are subject to variations caused by biological and technical effects. In a transcriptome study, systematic differences resulting from biological conditions are of interest, whereas technical variation should be minimal. The highest proportion of technical variation is systematic and potentially introduced by the RNA processing steps . In addition, RNA quality and sample storage time influence overall variation of transcriptomes . Therefore, it is mandatory to avoid batch effects wherever possible and to set up a suitable strategy for technical noise reduction after mRNA quantification. In the ideal experimental setting, all samples would be processed in a single batch. However, caused by technical limitations for the number of samples that can be processed at once, this is impossible when large sample sets are processed. For instance, RNA isolation can only be performed for a small number of samples in parallel. Amplification and labeling of RNA is usually carried out on well plates of 96 or 384 samples, and several of these plates are required for a large-scale transcriptome study. In addition, batch sizes of the scanning step are currently limited to 48 samples on the Affymetrix platform and 172 samples for Illumina. RNA quality, sample storage time and plate layout are important additional technical factors influencing the association analysis of gene expression data and common disease risk factors . Consequently, batch buy DAPT (GSI-IX) effects cannot be avoided in studies comprising a large number of subjects, and removal Rabbit Polyclonal to HES6 of these effects is necessary for reliable differential expression analysis. Technical factors, including batch effects, also affect longitudinal gene expression analysis. As RNA is collected buy DAPT (GSI-IX) at different time points in these studies, additional factors possibly influencing gene expression levels need to be considered. Depending on the time between measurements, the biochemistry of the assays, the scanning device and even the microarray technology may have changed. buy DAPT (GSI-IX) If samples from different time points are processed in parallel, storage time of samples might affect gene expression levels, leading to batch effects. Consequently, it is mandatory to reduce batch effects without eliminating biological variation and to demonstrate repeatability of gene expression levels. Several approaches have been proposed for batch effect removal from gene expression data [3C7]. Linear models can be applied to estimate batch effects between technical replicates measured at each time point. Resulting effect estimates can then be utilized for correcting overall gene expression levels between batches. An alternative regression approach is Deming regression , which allows to model normally distributed errors independently for two measurement methods. Passing-Bablok regression also models errors independently , but this approach does not introduce assumptions about the underlying error distributions. Workman and colleagues  reported that linear models are not capable to fully correct for batch effects and proposed the nonlinear method integrates quantile information of gene expression distributions and uses a cubic spline to fit all values dependent on signal intensities. combines location and scale adjustment with empirical Bayes to remove batch effects . Location and scale parameters, representing mean and variance, are estimated for each batch and each gene independently. Batch effects are estimated by empirical Bayes and used for batch effect removal. has been successfully applied to several datasets [3, 12C14], and using a single reference sample for each batch, its usefulness has been demonstrated for cross-sectional data . The aforementioned approaches assume that the batches are known. Different matrix factorization-based methods were developed for the case that unwanted factors of variation are unknown, e.g. surrogate variable analysis (SVA)  or removal of unwanted variation (RUV) . On microarrays, background noise is often modelled by negative control genes. These should not be differentially expressed between biological conditions. In contrast, observed differences between negative control genes can buy DAPT (GSI-IX) be considered as technical variation. RUV utilizes negative controls combined with technical replicates when estimating and correcting for batch effects (. To process Illumina iScan data from FU visit, they had.