Hello all,
I have combined two subsets of two different GSE datasets (One as Controls and One as Cases) and have made a new data frame. I see a complete separation between the two batches. So, I thought I should do the batch correction. But the batch indices and labels completely match. The resulting batch corrected dataset against those labels (which were the batches too) returned no DEGs. Would someone explain why this has happened and how I can get rid of the batch effect for this specific case, please? Thanks in advance.
•
written
by
ghiasirad.milad •
1 answer
If all cases belong to a batch, and all controls belong to a different batch, it is impossible to do a batch correction, because you can't know if the differences between the 2 groups are due to the batch, or to their experimental conditions (i.e. the conditions are "totally confounded"). And vice-versa: the same thing applies for any difference you may find between the 2 groups and think to be biological.
When you tried to correct the differences between the 2 batches, you cancelled-out the differences between the 2 groups (because they are the same thing), that's why you did not find any differences.
Log in to answer this question.
-
Covariate shift in gene expression datasets
written by Hargunjeet •
-
PCA Plotting Differences Before and After Batch Correction in RNA-seq for Meta-Analysis
written by Nelo •
-
Batch correction in RNAseq
written by Esraa •
-
Batch effects and what to do about them
written by Llander •
-
Modeling RNAseq batch effects using a non-case/control technical replicate
written by Chris Miller
-
Batch effect correction for bulk RNA-seq
written by bobbybobbobbo •
-
Differential Gene Expression after batch correction with DESC?
written by skjw1029 •
-
Can I run EdgeR or DESeq2 on bimodal data caused by batch effect?
written by jeltje.van.baren
-
Removing Batch effect that is the same as condition - DESEq2
written by annamariabugaj •
-
RNA-Seq Batch correction negative values
written by firestar
