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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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duplicate 'row.names' are not allowed #479

Open xiangyupan opened 1 year ago

xiangyupan commented 1 year ago

Hi, My expression matrix has several same gene names within it. When I run get_regulons(Aucell.loom), an error occured as follows: In open_loom(opt$input_loom) : Loom specification version 2 or smaller detected! Error in.rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed Calls: get_regulons ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<- In addition: Warning message: non-unique values when setting 'row.names': ‘A2M’, ‘A2ML1’, ‘A4GNT’, ‘AADAC’, ‘AANAT’, ‘ABCA1’, ‘ABCA13’, ‘ABCA4’, ‘ABCA5’, ‘ABCA9’, ‘ABCB11’, ‘ABCB5’, ‘ABCB9’, ‘ABCC1’, ‘ABCC10’, ‘ABCC2’, ‘ABCC3’, ‘ABCC5’, ‘ABCC8’, ‘ABCC9’, ‘ABCG1’, ‘ABCG2’, ‘ABHD10’, ‘ABHD15’, ‘ABHD17C’, ‘ABHD3’, ‘ABHD4’, ‘ABI1’, ‘ABI2’, ‘ABL1’, ‘ABLIM1’, ‘ABO’, ‘ABP/ZF’, ‘ABR’, ‘ABRA’, ‘ABRAXAS1’, ‘ABTB2’, ‘ACAA2’, ‘ACACB’, ‘ACAD11’, ‘ACADS’, ‘ACAN’, ‘ACAP2’, ‘ACBD6’, ‘ACCS’, ‘ACER1’, ‘ACLY’, ‘ACOT1’, ‘ACOT12’, ‘ACOT2’, ‘ACOT7’, ‘ACOX3’, ‘ACOXL’, ‘ACP2’, ‘ACP3’, ‘ACR’, ‘ACRBP’, ‘ACSBG1’, ‘ACSBG2’, ‘ACSF3’, ‘ACSS1’, ‘ACTB’, ‘ACTC1’, ‘ACTG1’, ‘ACTL6A’, ‘ACTL9’, ‘ACTN1’, ‘ACTN2’, ‘ACTR2’, ‘ACVR1C’, ‘ACY3’, ‘ACYP2’, ‘ADA’, ‘ADAD1 [... truncated] Execution halted

I am a little confused that it is normal to have same gene names in the human genome. It seems that the 10x scRNA-seq data mapped to the genome with same gene names which is also normally. So I am not sure whether should I dedup these multi appeared genes.

Hope to your reply. Best!

ghuls commented 1 year ago

Your expression matrix should only contain unique gene names.