different row counts implied by arguments

[wyt14]

I encountered the following problems when running. What do you think is the cause of the problem? Thank you very much.

res = do_pipeline(
+     out_path      ="...", 
+     counts_file_dir  = ".../polyAbam_counts/",
+     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 .../polyAbam_counts//BT1290.tab.gz
Loaded 23949 x 50 matrix of counts
Loading .../polyAbam_counts//BT1292.tab.gz
Loaded 0 x 0 matrix of counts
Error in DataFrame(cell = colnames(counts_matrix), barcode = cell_to_barcode[colnames(counts_matrix)], :
different row counts implied by arguments

[pfh]

Hi wyt14.

I'm finding it quite hard to read your example code. You can put your code in triple quotes to make it readable.

```
Example code.
```

I'm guessing the problem is something to do with the Loaded 0 x 0 matrix of counts.

[wyt14]

I'm very sorry. I have modified the code. The main issue is that my BT1290.tab.gz and BT1292.tab.gz were generated from the same batch of code. However, in function "do_pipeline", BT1290 loaded successfully, while BT1292 did not load successfully. I'm not sure what went wrong. I look forward to your response.

[pfh]

I would have a look at the those .tab.gz files. Is one of them empty?

Also whether your cells_to_use includes cells from both of them, and they are matching up with how cell_name_func is naming things.

[wyt14]

BT1290.tab.gz Content ：
gene cell count
GL000008.2_3067_f CCTTCCCGTCCGCTGA 1
GL000008.2_85625_f ACAGCCGCAAGACACG 1
GL000008.2_85625_f ATCACGAGTTAAGTAG 1
GL000008.2_85625_f GTGCTTCTCAAAGACA 1
GL000008.2_85625_f TGTATTCAGTCAAGGC 1
GL000009.2_128471_f CAGCTAAGTCGCGGTT 1

BT1292.tab.gz Content ：
gene cell count
GL000008.2_3067_f AGGGTGAAGCATCATC 1
GL000008.2_85625_f AAAGCAAAGGAATGGA 1
GL000008.2_85625_f ACGGAGAAGTAGGTGC 1
GL000008.2_85625_f ACTTGTTTCTTGACGA 1
GL000008.2_85625_f AGATCTGTCAAAGACA 1

barcode_total.txt Content ：
BT1290_AAACCTGGTCCATGAT-1
BT1290_AAACGGGTCGGCCGAT-1
BT1290_AAAGATGAGAGTAATC-1
BT1290_AAAGATGAGTATCGAA-1
BT1290_AAAGATGCAGGATCGA-1
BT1290_AAAGCAAAGCAGCGTA-1

code：

polyApiper:::do_ensembl_organism(
    out_path="human_ens100", 
    species="Homo sapiens", 
    version="100")

# Which cell names to use.
tsne <- read.csv("/data/polyApipe/LUAD/barcode_total.txt")
cells_to_use <- matrix(unlist(strsplit(tsne[,1],split="-")),ncol=2,byrow=T)[1:50,1]

# How cell names are constructed from batch name and cell barcode.
# Should match naming in cells_to_use.
cell_name_func <- function(batch,barcode) paste0(batch,"_",barcode)

# - Load output from polyApipe.py
# - Produce HDF5Array SingleCellExperiment objects containing counts
# - Perform further analysis steps
res = do_pipeline(
    out_path      ="/data/polyApipe/LUAD", 
    counts_file_dir  = "/data/polyApipe/LUAD/polyAbam_counts/",
    batch_names   =c("BT1290"),
    peak_info_file="polyAbam_polyA_peaks.gff", 
    organism      ="human_ens100",
    cells_to_use  =cells_to_use,
    cell_name_func=cell_name_func
    )

[pfh]

Ok, so are there any BT1292 cells in barcode_total.txt? If not perhaps just give the BT1290 filename, using counts_files rather than the counts_file_dir argument.

[wyt14]

Thank you very much for the reminder. I re-verified the barcode_total.txt file, and now BT1290 and BT1292 can be read normally. However, a new issue has arisen, and I look forward to your assistance. #7