Dear Bioconductor team,

I generated counts from star aligned bam using htseq and following the best practices to do differential expression using DESeq2.

Here is my sample information with condition & batch columns

Sample  condition   batch
sample_6M_C1    sample_6M_C B1
sample_6M_C2    sample_6M_C B1
sample_6M_C3    sample_6M_C B1
sample_6M_H1    sample_6M_H B1
sample_6M_H2    sample_6M_H B1
sample_6M_H3    sample_6M_H B1
sample_6M_M1    sample_6M_M B1
sample_6M_M2    sample_6M_M B1
sample_6M_M3    sample_6M_M B1
sample_3M_C1    sample_3M_C B3
sample_3M_C2    sample_3M_C B3
sample_3M_C3    sample_3M_C B3
sample_3M_H1    sample_3M_H B3
sample_3M_H2    sample_3M_H B3
sample_3M_H3    sample_3M_H B3
sample_3M_M1    sample_3M_M B3
sample_3M_M2    sample_3M_M B3
sample_3M_M3    sample_3M_M B3
sample_5D_C1    sample_5D_C B4
sample_5D_C2    sample_5D_C B4
sample_5D_C3    sample_5D_C B4
sample_5D_H1    sample_5D_H B4
sample_5D_H2    sample_5D_H B4
sample_5D_H3    sample_5D_H B4
sample_5D_M1    sample_5D_M B4
sample_5D_M2    sample_5D_M B4
sample_5D_M3    sample_5D_M B4

And when i run DESeq2 it is giving the below error

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,directory = outdir , design = ~ batch + condition)
Error in checkFullRank(modelMatrix) : 
  the model matrix is not full rank, so the model cannot be fit as specified.
  One or more variables or interaction terms in the design formula are linear
  combinations of the others and must be removed.

  Please read the vignette section 'Model matrix not full rank':

  vignette('DESeq2')

I have seen couple of discussions on the same error, but in my case error is due to adding batch effect to design.

Could you please help me to resolve this.

Thanks In Advance Fazulur Rehaman

Did you read the vignette section indicated?