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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data
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problem with example data #9

Closed fangling0913 closed 5 years ago

fangling0913 commented 5 years ago

I tried to run DoubletDecon with the example data to help me understand the tool. However, it always run into problem at the last step. The log was as follows:

Loading packages... [1] "ERROR: groupsFile must be a character string!" Reading data... Processing raw data... Combining similar clusters... Creating synthetic doublet profiles... svd calculated PCA Importance of component(s): PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14 R2 0.43 0.214 0.1879 0.06106 0.03477 0.01435 0.01032 0.0063 0.00577 0.0051 0.00375 0.00285 0.00212 0.00185 Cumulative R2 0.43 0.644 0.8319 0.89293 0.92770 0.94205 0.95237 0.9587 0.96444 0.9695 0.97329 0.97614 0.97826 0.98011

Attention: the number of pure cell types = 14 defined in the signature matrix;

PCA results indicate that the number of cell types in the mixtures = 1 Step 1: Removing possible doublets... svd calculated PCA Importance of component(s): PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 R2 0.5574 0.1895 0.07032 0.03336 0.02419 0.01826 0.01419 0.01346 0.00841 0.00629 0.0049 0.00432 0.00382 Cumulative R2 0.5574 0.7469 0.81724 0.85060 0.87479 0.89305 0.90724 0.92070 0.92911 0.93540 0.9403 0.94462 0.94844 PC14 R2 0.00343 Cumulative R2 0.95187

Attention: the number of pure cell types = 14 defined in the signature matrix;

PCA results indicate that the number of cell types in the mixtures = 1 Step 1: Removing possible doublets... svd calculated PCA Importance of component(s): PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 R2 0.5574 0.1895 0.07032 0.03336 0.02419 0.01826 0.01419 0.01346 0.00841 0.00629 0.0049 0.00432 0.00382 Cumulative R2 0.5574 0.7469 0.81724 0.85060 0.87479 0.89305 0.90724 0.92070 0.92911 0.93540 0.9403 0.94462 0.94844 PC14 R2 0.00343 Cumulative R2 0.95187

Attention: the number of pure cell types = 14 defined in the signature matrix;

PCA results indicate that the number of cell types in the mixtures = 1 Step 2: Re-clustering possible doublets... Step 3: Rescuing cells with unique gene expression... Error in colnames<-(*tmp*, value = c("clusterNr", "clusterName", "cellName")) : attempt to set 'colnames' on an object with less than two dimensions In addition: Warning messages: 1: In if (!is.null(v) && is.atomic(x[[jj]]) && !is.null(names(x[[jj]]))) names(x[[jj]]) <- NULL : closing unused connection 3 (C:\Users\fangl\Downloads\software\DoubletDecon-master\PBMC_example.log) 2: In reclust_groups$cells <- row.names(reclust_groups) : Coercing LHS to a list

Can someone helps me? Thanks Linda

EDePasquale commented 5 years ago

This issue should be corrected now. Seurat_Pre_Process outputs a matrix but the command line version of DoubletDecon expects a data.frame. The UI version, however, needs a matrix format so I convert to data.frame internally when it is needed in the command line version. Please let me know if this or other problems persist.