MuSiC2 issue: Error in MOD0 + mod0 : non-conformable arrays

[jaclynbeck-sage]

Running music2_prop, the following issue happens if 'select.ct' argument = NULL. It's allowed to be NULL in the original music_prop, and a NULL value means "use all cell types in the metadata" for that function. The documentation for music2_prop also says this. However there's no check or logic for the case where select.ct = NULL in music2_prop, so when it gets to the iteration loop it creates a MOD0 matrix with 0 rows:

ncell = length(select.ct) # returns 0 for select.ct = NULL
...
MOD0 = MOD1 = matrix(0L, nrow = ncell, ncol = length(exp_genel))

I can get around this by putting an actual value for select.ct when calling the function, however, could you change the documentation to match the code, or code to match documentation?

[jaclynbeck-sage]

Also this same issue appears in music2_prop_toast and music2_prop_t_statistics.

[spatts14]

Hi @jaclynbeck-sage, what exactly you put for the select.ct value? Im assuming you just put all the cell types once, not label a list per cell - correct? Does it need to in the form of a list? It looks like they did update it to be c("Cell type", "etc").

I got this error: Error in MOD0 + mod0 : non-conformable arrays
Calls: music2_prop_t_statistics

So Im trying to trouble shoot it . I had it set as NULL so it would use the single cell as default. Just double checking as this takes me a long time to run!

[jaclynbeck-sage]

@spatts14 Yes, I just put a vector of cell types: c('type1', 'type2', 'type3', ..., 'typeZ') (unique values, not a list per cell). That seemed to work ok.

[JoyOtten]

Hi I still have the same problem even when I put the cell types in a character vector.

[gevro]

Hi, I am getting the same issue.

[JoyOtten]

Hi, I think this issue has to do with the construction of your datasets. See here the code that I used for MuSiC (v1) version https://github.com/klengellab/Ska2/blob/main/Deconvolution_MuSic.R
This worked for me.

[gevro]

Thanks, but the issue is specific to music2 functions. Music v1 works fine. So your code I don't think helps this issue.

[rob-meller]

Has there been any resolution to this issue.? When I run my two data sets individually through MuSiC using a vector of cell_types, they work. Then I run them together with MuSiC2 we get the "Error in MOD0 + mod0 : non-conformable arrays". THX