I attempt to calculate differential expression using DESeq2. I used my BAM files (from TOPHAT) and gff3 annotation table to create a SummarizedExperiment (se_2).
I also tried using the example "airway" data set and obtain similar error: "Error in x %*% Rinv : requires numeric/complex matrix/vector arguments". If use rlog() or DESeq() I obtain this error. It seems you have this error if you use a dataframe instead of a matrix (see the link). In my case I did not change the object class.
I rebuilt the "DESeq2" package and it did not solve the problem.
>sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
>se_2
class: SummarizedExperiment
dim: 59225 12
exptData(0):
assays(1): counts
rownames(59225): Bo00285s010 Bo00285s020 ... Bo9g186200 Bo9g186210
rowData metadata column names(0):
colnames(12): 511_T2_Late_Wood 513_T2_Early_Wood ... 569_T8_Late_Camb 571_T8_Early_Camb
colData names(5): stade plant SampleName Bam.file file
> dds <- DESeqDataSet(se_2, design = ~ stade)
> rld <- rlog(dds)
Error in x %*% Rinv : requires numeric/complex matrix/vector arguments
Thanks for your help. Please let me know if I did not give enough information. Nico
