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• Using ComBat on RNASeq FPKM counts
  I want to apply ComBat function in the sva package to an RNA-Seq dataset containing FPKM values. ...
• Should batch correction be performed before or after feature selection in scRNA-seq
  Hi, I am analysing some Smart-seq2 data. The data comes from multiple plates, so I want to remo...
• Normalization and batch effects correction in RNA-Seq data
  Hi guys, I have a simple question. I have RNA-Seq data from different batches. As suggested looki...
• batch effect after using comBat
  Hi! I am analyzing data from RNA-seq. I have six groups: group1 (batch1), group2 (batch 1 + batc...
• Using ComBat-seq on transcript counts
  I am working with transcript counts produced by RSEM which gives me expected_count, TPM and FPKM ...
• Should I pre-normalize RNAseq data before combat?
  Hello, I want to use combat to remove batch effct. The format of rnaseq data is counts from RSEM....
• ComBat before or after Probe filtering ????
  Hi,   I  am planning to preprocess 40 microarray series comprising of 1200 samples. For all thes...
• How do you evaluate the effectiveness of the batch effect algorithm?
  After homogenizing microarray gene expression data with a batch effect correction algorithm, such...
• Normalizing For Batch Effect In RNA-Seq Data
  Hello,  Does anyone have a suggestion for dealing with "batch effect" between two batches of sma...
• Methods for analyzing and correcting RNA-seq dataset balance
  I’m working with an imbalanced set of cell line RNA-seq data with small group sizes. For example,...
• Differential expression on Combat-adjusted FPKM
  I have RNA-seq for 62 samples from 4 groups sequenced in 2 known batches, with a clear batch-effe...
• Batch correction in DESeq2
  For RNA-seq data analysis using DESeq2, a recommended method for batch effect removal is to intro...
• At Which Step Apply A Detection Filter When Preprocessing Microarray Data? (Before/After Normalization, Batch Effects Removal)
  Hi all, I am trying to understand what is the best practice when preprocessing microarray data us...
• In Which Type Of Data Does Combat Best Perform?
  Hi all, I have read Johnson et al. about ComBat and usage but I am unsure about best practices on...
• combat correction or include batch effect in the model?
  I am performing differential expression analysis using RNA-seq data. I am using limma package. I...
• Batch-correction on tximport data from salmon
  Hello, I am analyzing two disting BioProjects together from SRA. My pipeline was: Fastp > sal...