I am attempting to do a DEA analysis of matched paired BRCA normal tumour samples using TCGAbiolinks. When I do an analysis of my samples using this formula

```
dataDEGsMatched <- TCGAanalyze_DEA(mat1 = MatchedTPdataFilt,
mat2 = MatchedNTdataFilt,
Cond1type = "Tumor",
Cond2type = "Normal",
fdr.cut = 0.01,
logFC.cut = 1.5,
method = "glmLRT")
```

It works and returns a DEG, however, I do not believe it is matched paired. When I add in the line paired = TRUE I get the following error.

```
> dataDEGsMatched <- TCGAanalyze_DEA(mat1 = MatchedTPdataFilt,
+ mat2 = MatchedNTdataFilt,
+ Cond1type = "Tumor",
+ Cond2type = "Normal",
+ pipeline = "edgeR",
+ fdr.cut = 0.01,
+ logFC.cut = 1.5,
+ method = "glmLRT",
+ paired = TRUE)
Batch correction skipped since no factors provided
----------------------- DEA -------------------------------
there are Cond1 type Tumor in 113 samples
there are Cond2 type Normal in 113 samples
there are 14477 features as miRNA or genes
I Need about 0 seconds for this DEA. [Processing 30k elements /s]
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
```

I don't really understand what is causing this error. I have tried to ensure the matrices are both in the correct order so the corresponding columns are paired using -

```
MatchedTPdataFilt <- MatchedTPdataFilt[, order(colnames(MatchedTPdataFilt))]
MatchedNTdataFilt <- MatchedNTdataFilt[, order(colnames(MatchedNTdataFilt))]
```

But this doesn't fix the problem.

I also attempted to then change the column names for the matrices so the corresponding names match, but this then returned a different error.

```
colnames(MatchedTPdataFilt) <- (1:113)
colnames(MatchedNTdataFilt) <- (1:113)
> dataDEGsMatched <- TCGAanalyze_DEA(mat1 = sort(AllMatcheddataFilt[,samplesMatchedTP]),
+ mat2 = sort(AllMatcheddataFilt[,samplesMatchedNT]),
+ Cond1type = "Tumor",
+ Cond2type = "Normal",
+ pipeline = "edgeR",
+ fdr.cut = 0.01,
+ logFC.cut = 1.5,
+ method = "glmLRT",
+ paired = TRUE)
Error in names(x) <- value :
'names' attribute [7] must be the same length as the vector [1]
```

I have also checked that the dimensions for both matrices are the same -

```
> dim(MatchedNTdataFilt)
[1] 14477 113
> dim(MatchedTPdataFilt)
[1] 14477 113
```

I have read the manuals and user guides for TCGAbiolinks and haven't managed to shed any light on the issue, I would appreciate any help.

Thank you.

Hello again, can you show how you create the

MatchedTPdataFiltandMatchedNTdataFiltobjects? I just want to re-create the error on my own system. Is it somewhat a continuation of the issue in your other question ( A: Matched Paired Tumour-Normal DEA of BRCA using data downloaded using TCGAbiolink )?Hello! Yes it is a continuation from that. I used a workflow for TCGAbiolinks to process the matched data. I have used it before for unmatched normal-tumour samples and it has worked.

Here is what I have used -

Okay, I have managed to reproduce the exact same error.... now let me see if I can solve it.

Posted an answer below