search

zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
327 stars 70 forks source link

error in RunCellQC #213

Open yangtao38324 opened 7 months ago

yangtao38324 commented 7 months ago

After I built the Seurat object with raw_counts, I encountered the following error when running CellQC

srt <- RunCellQC(srt, return_filtered = FALSE) Warning in RunCellQC(srt, return_filtered = FALSE) : Data type is not raw counts! Error in RunDoubletCalling(srt = srt, db_method = dbm, db_rate = db_rate) : Data type is not raw counts! head(srt@assays$RNA@counts) 6 x 1988 sparse Matrix of class "dgCMatrix" [[ suppressing 60 column names ‘AAACCTGAGACAGACC’, ‘AAACCTGAGATGGGTC’, ‘AAACCTGCAAGCCATT’ ... ]]

SOX17 . . . . . . . . . . . . . . MRPL15 . . 0.5179662 . . . . 0.7895499 0.3860846 . 0.6794109 . 0.4686949 . LYPLA1 . . 0.5179662 . 0.6911035 . . . 0.3860846 . . . . . TCEA1 . 0.8431292 0.5179662 0.8298575 0.6911035 1.544280 . 0.7895499 0.3860846 0.8910172 0.3963286 . 0.7865531 . RGS20 . . . . 1.0958864 . . . 0.6639337 . 0.3963286 . . . ATP6V1H 0.8125308 0.8431292 0.5179662 . . 1.044613 . 0.5886769 . . 0.3963286 . . .

SOX17 . . . . . . . . . . . . . . . . .
MRPL15 0.9531057 . . 0.6127239 . 0.5938594 1.27276 0.9001453 . 1.1160677 . . . . 0.669189 . 1.012636 LYPLA1 0.9531057 . . 0.6127239 . . . . . . . . 1.211492 . . . .
TCEA1 0.9531057 . 0.9816634 . . . 1.27276 0.9001453 . 0.8622783 . . 1.211492 1.014313 . . .
RGS20 . 1.393158 . . . . . . . 0.5213354 . . . . . . .
ATP6V1H . . 1.4673636 . . . . . . 0.5213354 . . . . . . 1.012636

SOX17 . . . . . . . . . . . . .
MRPL15 . . 1.172029 0.8089216 0.6574164 0.5132103 0.5481716 . 0.8762200 0.344825 . 1.2094253 1.385919 LYPLA1 . . . . . . 0.3111863 . . 0.344825 . 0.7773867 .
TCEA1 1.296574 . 0.442847 . 1.0506818 0.8507028 1.0385852 1.0742843 0.3834021 0.600750 . 1.2094253 .
RGS20 . 0.8369941 . . . . 0.5481716 . . . . . .
ATP6V1H . . 0.442847 . 0.6574164 0.5132103 0.3111863 0.6749569 0.3834021 . . 0.7773867 1.385919

SOX17 . . . . . . . . . . . . . . . . ...... MRPL15 0.7472144 . 0.5936053 . 0.557577 . 0.6697472 . . . 0.6690961 . . 1.014257 . . ...... LYPLA1 . . . 0.4990813 . . . . . . . 0.6824708 . . . . ...... TCEA1 0.7472144 . . . . . 0.6697472 . . . 0.6690961 . . 1.507323 . . ...... RGS20 . . 0.5936053 . 0.557577 . 1.0672891 . . . . . . . . 0.6283463 ...... ATP6V1H 0.7472144 . 0.5936053 0.4990813 0.557577 . . 0.613034 . 0.4741964 . . . . . 0.6283463 ......

.....suppressing 1928 columns in show(); maybe adjust 'options(max.print= , width = )' ..............................

MInsYang commented 2 months ago

Hello, I have reviewed the SCP code, and the cause might be that the Seurat object you provided does not have a counts matrix under the RNA assay. The RunDoubletCalling function first checks status <- check_DataType(srt, slot = "counts", assay = assay).