Hi,

I've got an error in a DESeq2 analysis by running code:- dds <- DESeqDataSetFromMatrix(countData = countData, colData = coldata, design = ~ Conditions + Treatment_time + Conditions:Treatment_time) and got this error:- Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified. Levels or combinations of levels without any samples have resulted in column(s) of zeros in the model matrix.

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

vignette('DESeq2') In addition: Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors please help if anybody have any idea.

Is this the same as https://www.biostars.org/p/9477180/#9562146 ?

If so then it's odd because the design is full rank and should work. Make sure that no variables are overwritten in your script, restart R, make the script clean and try again, it should work. Please get used to make reproducible examples. colData via dput() is a good idea.