Good day,

Please help with batch option in Deseq2, I have the error below and can't understand the problem as for me my METADATA_RAT has nessesary columns

txi.salmon_rat ENSRNOG00000000070 1.276541e+02 1.296898e+02 1.332189e+02 1.133108e+02 1.110791e+02 1.381127e+02 ENSRNOG00000000073 3.887378e+01 4.370201e+01 4.711458e+01 3.889587e+01 3.678910e+01 4.497496e+01 ENSRNOG00000000075 7.934947e+01 6.401462e+01 6.494397e+01 8.041880e+01 7.816325e+01 7.012191e+01....

coldata_rat <- data.frame(batch = as.factor(METADATA_RAT$batch)) METADATA_RAT$batch [1] "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" [8] "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" "PRJNA953086" .....

dds_rat_with_batch <- DESeqDataSetFromTximport(txi.salmon_rat, colData = coldata_rat, design = ~ batch + condition) Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData

Could you please help with it,

Galina

Your code is poorly readable. Suggest you select and then highlight with markdown using the 10101 button.

Generally, colData(dds) must have all the columns you reference in design. Here, it is only batch. condition is missing.