Error in DESeqDataSetFromMatrix /.../ ncol(countData) == nrow(colData) is not TRUE

Question

[Nick]

Hey all,

I'm kind of at my wit's end here... I know other's have posted similar errors, and I've eliminated the trivial (extra column) type causes.

> ddsPlin2wtvsko <- DESeqDataSetFromMatrix(countData=countData, colData=metaData2,
 design=~genotype, tidy = TRUE)

Error in DESeqDataSetFromMatrix(countData = countData, colData = metaData2,  : 
  ncol(countData) == nrow(colData) is not TRUE

> all(colnames(countData) == rownames(metaData2))

TRUE

> class(countData)

"matrix" "array" 

> class(metaData2)

"matrix" "array" 

> dim(as.matrix(countData))

54309     8

> dim(as.matrix(metaData2))

8 4

> all(colnames(countData) == rownames(metaData2))

TRUE

Why am I getting an "ncol(countData) == nrow(colData) is not TRUE" error?!?

Answer 1

[swbarnes2]

The quick thing to try: try tidy = FALSE

[Nick]

You, beauty! I'm totally baffled as to why there was an error, but at least I've moved past the banging head against wall stage.

> ddsPlin2wtvsko <- DESeqDataSetFromMatrix(countData=countData, colData=metaData2 design=~genotype, tidy = FALSE)

converting counts to integer mode
Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors

[swbarnes2]

Those messages are not problems. You want raw counts to be integers, and you probably want your design elements to be factors.