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navinlabcode / copykat

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WARNING! NOT CONVERGENT! #98

Open stroke1989 opened 11 months ago

stroke1989 commented 11 months ago

Hi, Thanks for this tool, when I used copykat to analyze my scRNAseq data, I got warnning as below: epn_2 = read_rds(file = "epn_2_postfilter.rds") epn_2.rawdata <- as.matrix(epn_2@assays$RNA@counts) epn_2.copykat.result <- copykat(rawmat=epn_2.rawdata, id.type="S", ngene.chr=5, win.size=25, KS.cut=0.1, sam.name="epn_2", distance="euclidean", norm.cell.names="",output.seg="FALSE", plot.genes="TRUE", genome="hg20",n.cores=60) [1] "running copykat v1.1.0" [1] "step1: read and filter data ..." [1] "24856 genes, 9037 cells in raw data" [1] "8924 genes past LOW.DR filtering" [1] "step 2: annotations gene coordinates ..." [1] "start annotation ..." [1] "step 3: smoothing data with dlm ..." [1] "step 4: measuring baselines ..." number of iterations= 297 number of iterations= 367 number of iterations= 165 number of iterations= 449 number of iterations= 297 number of iterations= 264 [1] "low confidence in classification" [1] "cell: 1" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 2" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 3" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 4" number of iterations= 168 [1] "cell: 5" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 6" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 7" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 8" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 9" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 10" WARNING! NOT CONVERGENT! number of iterations= 500 [1] "cell: 11" WARNING! NOT CONVERGENT! number of iterations= 500

could anyone help me out? Appreciate!

hyq9588 commented 10 months ago

I met the same question

mbihie commented 10 months ago

Did you find an answer?

RijndertAriese commented 9 months ago

I encountered the same problem, unfortunately. Does anyone have an idea on what the cause of this warning is and/or what it means for the output?

zhangsiyao618 commented 7 months ago

https://github.com/navinlabcode/copykat/issues/26, I encountered the same problem, maybe this reply will help ?