Some question about running error in the tutorial

yycunc / iSMNN

iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement

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Some question about running error in the tutorial #2

Open HelloWorldLTY opened 2 years ago

HelloWorldLTY commented 2 years ago

Hi, sorry to disturb you. I try to run the tutorial listed in the readme page, and then I found a problem existing in the label harmony step.

For the first part is the typo.

For this code, I think "data_SMNN" should be "data_iSMNN". But after I correct it, I still receive this error:

Could you please help me? Thanks a lot.

yycunc commented 2 years ago

Sorry for the mistake I made in the tutorial. Actually, I updated the unifiedClusterLabelling function of SMNN package, but I forgot to update the tutorial here. It should be:

batch.cluster.labels <- unifiedClusterLabelling(batches = list(data_iSMNN$batch1.mat, data_iSMNN$batch2.mat), features.use = markers, cluster.labels = cluster.info, min.perc = 0.3)

I have corrected it in the README. Now it should work well. Thanks for your comment!

Yuchen