Hi,

I get the following error message on combining this dataset I have using the following command:

MSnset_comb_norr <- MSnbase::combine(MSnset_Set1,MSnset_Set2,MSnset_Set3,MSnset_Set4)

Error in combine(x[[nm]], y[[nm]]) : 
  matrix shared row and column elements differ: Mean relative difference: 0.4045317

The error occurs if I combine MSnsetSet4 as it works fine till MSnsetSet3.

For Reference the object dimensions are as below

dim(exprs(MSnset_Set4))
 12426    10

dim(exprs(MSnset_Set3))
 13260    10

dim(exprs(MSnset_Set2))
 11117    10

dim(exprs(MSnset_Set1))
 11973    10

This is first time I am getting this message as the combine function works fine otherwise. Any suggestions regarding this would be highly appreciated.

Thanks.

Kamal

From the dimensions of your 4 objects, I assume that the 10 sample (column) names are identical and that you want to combine along to features (rows). Could it be that MSnset_Set4 has a feature that exists in a previous object? This would indeed lead to such an error.

The column names are not identical. I am combining about 40 different samples based on the common peptides shared among them. Features (rows) represents peptides.