I am using SCnorm to normalize my gene_counts matrix.
I have 107 samples(4 conditions, each has 57, 19, 18, 13 samples)
I used these codes to see the count-depth relationship:
Conditions = rep(c(1,2,3,4), each= 57, 19, 18, 13)
countDeptEst <- plotCountDepth(Data = d, Conditions = Conditions, FilterCellProportion = .1, NCores = 3)
But I got this mistake
Error in plotCountDepth(Data = d, Conditions = Conditions, FilterCellProportion = 0.1, :
Number of columns in expression matrix must match length of conditions vector!
I'm sure that I have the right number of columns of the matrix.
1 answer
I'm sure that I have the right number of columns of the matrix.
Are you sure you have the right number of elements in the condition vector, because this statement doesn't make sense to me:
Conditions = rep(c(1,2,3,4), each= 57, 19, 18, 13)
each= takes one numeric argument. I think you're looking for:
Conditions = c(rep(1,57), rep(2,19), rep(3,18), rep(4,13))
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