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?!?
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
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