'x' must be an array of at least two dimensions

wyt14 commented 4 months ago

Dear author, I encountered the following error while running the command. Could you please provide me with some guidance? Thank you.

> res = do_pipeline(
+     out_path      ="/data/polyApipe/LUAD", 
+     counts_file_dir  = "/data/polyApipe/LUAD/polyAbam_counts/",
+     batch_names   =c("BT1290","BT1291"),
+     peak_info_file="polyAbam_polyA_peaks.gff", 
+     organism      ="human_ens100",
+     cells_to_use  =cells_to_use,
+     cell_name_func=cell_name_func
+     )

-- 1/4 load -- Loading /data/polyApipe/LUAD/polyAbam_counts//BT1290.tab.gz Loaded 139654 x 1276 matrix of counts
Loading /data/polyApipe/LUAD/polyAbam_counts//BT1291.tab.gz Loaded 180737 x 1292 matrix of counts
-- 2/4 assign -- -- 3/4 weitrices -- 422517 peaks in 2568 cells Error in rowSums(assay(peaks_se_relevant, "counts")[, good_cells, drop = F] > : 'x' must be an array of at least two dimensions In addition: Warning message: In .merge_two_Seqinfo_objects(x, y) : Each of the 2 combined objects has sequence levels not in the other:

in 'x': chrM, GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000213.1, GL000216.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, KI270330.1, KI270438.1, KI270442.1, KI270466.1, KI270467.1, KI270512.1, KI270706.1, KI270707.1, KI270708.1, KI270709.1, KI270711.1, KI270712.1, KI270713.1, KI270714.1, KI270717.1, KI270719.1, KI270720.1, KI270722.1, KI270725.1, KI270726.1, KI270727.1, KI270728.1, KI270729.1, KI270730.1, KI270732.1, KI270733.1, KI270734.1, KI270735.1, KI270736.1, KI270737.1, KI270742.1, KI270743.1, KI270744.1, KI270745.1, KI270746.1, KI270750.1, KI270752.1, KI270754.1, KI270755.1, KI270756.1
in 'y': chrMT, chrCHR_HG107_PATCH, chrCHR_HG109_PATCH, chrCHR_HG126_PATCH, chrCHR_HG1277_PATCH, chrCHR_HG1298_PATCH, chrCHR_HG1309_PATCH, chrCHR_HG1311_PATCH, chrCHR_HG1320_PATCH, chrCHR_HG1342_HG2282_PATCH, chrCHR_HG1362_PATCH, chrCHR_HG1384_PATCH, chrCHR_HG1395_PATCH, chr [... truncated]

pfh commented 3 months ago

My only guess is: polyApiper assumes the ENSEMBL naming convention for chromosomes, ie no "chr" in the name. You might need to do some hacking to achieve this.

I have to apologise, this project is on hiatus, I don't think I'm going to be much more help as I don't have time to maintain it at the moment.

shimi-ly commented 3 months ago

Hi, I'm experiencing the same error message, have you solved it yet?

MonashBioinformaticsPlatform / polyApipe

'x' must be an array of at least two dimensions #7