**0**wrote:

Hello!

I have followed the example reported in edgeR guideline, section "4.1 RNA-Seq of oral carcinomas vs matched normal tissue". I have 54 pairs of tumor and normal matched samples (therefore 108 samples in total).

The matrix reporting the counts in each sample is called "count_matrix".

> y <- DGEList(counts = count_matrix) > y <- calcNormFactors(y)

I created the data frame pheno in order to obtained the design matrix:

These are the first lines of my data.frame "pheno":

> head(pheno) Sample Patient Tissue 7 A1FG-11B A1FG N 50 A1EN-11A A1EN N 30 A2FF-11A A2FF N 58 A203-01A A203 T 41 A0AZ-11A A0AZ N 44 A0C3-11A A0C3 N > dim(pheno) [1] 108 3

This is the definition of the design matrix:

design <- model.matrix(~pheno$Patient+pheno$Tissue) rownames(design) <- colnames(count_matrix) y <- estimateDisp(y design, robust=TRUE) fit <- glmFit(y, design) lrt <- glmLRT(fit) topTags(lrt) Coefficient: pheno$TissueT logFC logCPM LR PValue FDR ENSG00000123500 7.608219 6.781840 537.6956 5.980826e-119 9.183558e-115 ENSG00000099953 6.165488 7.402075 490.9502 8.852279e-109 6.796337e-105 ENSG00000230838 6.582381 2.203078 395.0187 6.688333e-88 3.423312e-84 ENSG00000249669 -4.607226 4.389790 366.2898 1.202373e-81 4.615609e-78 ENSG00000119771 -3.010243 4.036926 357.9115 8.023370e-80 2.463977e-76 ENSG00000122641 3.525087 5.962757 316.3896 8.857866e-71 2.266876e-67 ENSG00000106004 -3.087477 3.386670 315.5859 1.325620e-70 2.907843e-67 ENSG00000165197 -5.792541 4.231021 307.6019 7.271719e-69 1.395715e-65 ENSG00000197576 -2.819078 1.514075 300.5615 2.485681e-67 4.240848e-64 ENSG00000090889 4.159287 4.095254 299.3114 4.653633e-67 7.145653e-64

When I do the following command I get an error:

```
summary(decideTests(lrt))
Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), :
dims [product 61420] do not match the length of object [18]
```

What'd I do wrong?

Thank you in advance

Fix the tag (it should be

edgeR) otherwise the maintainers won't get notified.18k