I have RNAseq from three treatments (A, B, C), each with biological replicates ran in two batches (batch1 with A & B; batch2 with C). Unfortunately, the batch effects are fully confounded with the condition (e.g., to compare A vs. C). Here, I understand it is impossible to separate the batch effects from the treatment, regardless of what statistical method I use. I thought of methods such as ComBat, removeBatcheffect (limma) but can not estimate covariates to include in the batch correction. Then thought of using the control-genes based methods such as RUVg-method; however I do not have ERCC control genes in the data or an independent data set of similar treatments to obtain the negative (or positive) control genes. I understand best would be to redo the experiment with good design. With that said, I am curious if anyone have suggestions or options that I can explore and be able to use the data in some way? Appreciate your help. Thank you.