Sentence examples for batch correction of the from inspiring English sources

Batch correction of the samples was performed using the ComBat package in R (19).

In fact, correlation between microarray and nCounter measurements remained globally unchanged with batch correction of the CD4 and CD14 microarray datasets.

For Batch correction of the patient data (Table  2), the Empirical Bayes' (EB) method ComBat was used (non-parametric prior method) [ 5].

For batch correction of microarray data, the non-parametric prior method of ComBat was used, which represents an Empirical Bayesian (EB) method [ 35].

Otherwise, the ComBat method70 was used for batch correction on the whole transcriptome of selected cells, and then we repeated steps (2)–(4) using ComBat-corrected data and used new PCs for clustering analysis.

These findings show that ComBat is highly suitable for batch correction of data derived from small sample sizes and does not lead to inappropriate modification of the underlying data as previously published [ 2].

The application of batch correction allowed the unequivocal identification of genes differentially expressed between RA and OA and returned the top-ranked GO category "extracellular matrix structural constituent" (8/74 genes; p-value decreased by 4 orders of magnitude).

The resulting distances can be interpreted as the dissimilarity of the arrays Before batch correction, the normalized data formed clear clusters for the different batches (7 different acquiry dates for groups of 2 – 4 individual Affymetrix chips; Figure  1a).

Of the published approaches for batch correction, the algorithm "Combating Batch Effects When Combining Batches of Gene Expression Microarray Data" (ComBat) appears to be most suitable for small sample sizes and multiple batches.

Following batch correction with ComBat the number of differentially expressed genes identified in the two groups was more consistent (260 and 211) and the overlap, in terms of probes reported in both groups, increased from just 11.6% to 66.4%, however the use of mean-centred data only increased the overlap marginally to 15.2% (Table 1, Figure 6, and Additional Files 3 and 4).

Results supported the correctness of the batch correction operations and cell type assignments from the integrated analysis.