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Hello from GenomeSpace! In this video step we will attempt to remove batch effects from our gene expression dataset using the ComBat module in GenePattern. From the Modules tab search or browse for the ComBat module. ComBat requires continuous gene expression data such as microarray intensity. Thus, we previously converted our discrete RNA-Seq count data to the continuous log counts-per-million unit using the PreprocessReadCounts module. We access the outputs from the PreprocessReadCounts module under the Jobs tab. Click and drag the gene expression file, in this case GSE63412GSE44229.logcpm.gct, to the input file field. ComBat also requires a sample information file that annotates the samples for the batch covariates as well as covariates of interest. From the GenomeSpace tab, click and drag a sample info file such as GSE63412GSE44229.sample.info.txt to the sample info file field. We will be using the parametric prior method. If the parametric estimates are poor, we can rer
