Error in cor.res[pos.lrs[t, 1], ] in spaCI_preprocess

[ayumatsubo]

Hi,

Thank you for your useful and interesting method.

I tried to perform spaCI for my own CosMx dataset, and I successfully loaded the st_expression and st_meta file, but when I ran the spaCI_preprocess function, it gave an error Error in cor.res[pos.lrs[t, 1], ] : subscript out of bounds.

The number of cells in st_expression and st_meta matched.

My code is following and I think the requirement was installed correctly.

spaCI_preprocess(st.exp = st.exp, st.meta = st.meta, LRdb = LRdB, K=k, cutoff=cut, dir=dir, cor_eval='pearson')

Or, do you have the docker container to perform this analysis?

Thank you for advance.

[akramayman]

Hello @ayumatsubo , I faced the same issue did you get any way to solve the problem? where my count and meta data is in the correct format and I used the CellChat database as LR database, k=5 and p cuttoff= 0.01.

Rscript spaCI/src/spaCI_preprocess.R MS_counts_matrix.csv MS_meta.csv 5 0.01 CellChatDB.mouse.rds 'pearson' "output directory"

@QSong-github @jing-su @tonyyang1995