Error in buildXYData

[sarah872]

Hi!

I am getting an error when running glimmaMA():

0 of 49 genes were filtered out in DESeq2 tests
Error in buildXYData(table, status, main, display.columns, anno, counts,  : 
  Length of groups must be equal to the number of columns in counts.

Here's my full code, I am starting with a counts table from featureCounts:

my_counts <- read.table("featurecounts.txt", header = TRUE, row.names=1)
my_counts$Chr <- NULL
my_counts$Start <- NULL
my_counts$End <- NULL
my_counts$Strand <- NULL
my_counts$Length <- NULL

my_columns=data.frame(row.names=as.vector(colnames(my_counts)), as.vector(colnames(my_counts)))
colnames(my_columns) = "treatment"
my_columns$treatment = substr(my_columns$treatment,1,nchar(my_columns$treatment)-1)
my_columns$treatment = as.factor(my_columns$treatment)

dds <- DESeqDataSetFromMatrix(countData=my_counts, colData = my_columns, design = ~0 + treatment)
DEanalysis <- DESeq(dds)

glimmaMDS(dds) # This works well
glimmaMA(DEanalysis) # This gives me the error

I'm attaching a subset of my featurecounts.txt.

[hasaru-k]

Hey @sarah872! Sorry for the belated response - could you potentially attach a small subset of the data, so we could reproduce this 🙏