Dear all, I have faced a problem with DESeqDataSetFromMatrix() function in DeSeq2. Here are a few rows of my coldata file.
Condition Type Patient1 Cancer TCGA-13 Patient2 Cancer TCGA-24 Patient3 Cancer TCGA-24 Patient4 Cancer TCGA-24 Patient5 Cancer TCGA-24 Patient6 Cancer TCGA-31 Patient7 Cancer f4034d75-d533
and the following are a last few rows of it:
Normal171 Normal GTEX-171 Normal172 Normal GTEX-172 Normal173 Normal GTEX-173 Normal174 Normal GTEX-174 Normal175 Normal GTEX-175 Normal176 Normal GTEX-176 Normal177 Normal GTEX-177 Normal178 Normal GTEX-178 Normal179 Normal GTEX-179 Normal180 Normal GTEX-180
DESeqDataSetFromMatrix() function produced the following errors:
converting counts to integer mode 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') In addition: Warning message: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors
I changed the Type column in to 1 and 2 for tumor and normal samples, however I got the same error. Can you guide me how to solve this problem?