Entering edit mode

10 months ago

nazaninhoseinkhan
▴
510

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?

Regards

Nazanin

What is your design?

Here is the command I used and got the error

It's not possible. Each patient has a unique ID, so condition is nested with itself. You cannot correct anything here, all cancer is TCGA and all normals is GTEX, is is confounded by that.