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error in gap statistic #5
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Sure, please send it to me.
…On Wed, Aug 22, 2018 at 7:30 AM, Timothy Daley ***@***.***> wrote:
Error in distMatrix[medoid, which(cluster == medoid)] :
subscript out of bounds
@linzx06 <https://github.com/linzx06> : do you know what this means? What
can I do to debug the issue? The data is from the Buenrostro hematopoietic
scATAC-seq data. I can send it to you if that'll help.
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cellNames2.txt<https://office365stanford-my.sharepoint.com/:t:/g/personal/tdaley_stanford_edu/EYhMbxfDQ91Gs_Bef8lR2uUBz_0qAxpXikrGDwXb-5xlYA>
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scATACseq_counts2.txt.bz2<https://office365stanford-my.sharepoint.com/:u:/g/personal/tdaley_stanford_edu/EWHFvxm-c6NFqTamrPHGj90BQ5utIPdsnkipw_ZTRpBWsw>
The matrices are attached. The code to load and run gap stat is given below.
scATACseqCounts = as.matrix(Matrix::readMM("scATACseq_counts2.txt"))
cellNames = scan("cellNames2.txt", what = "chraracter()")
colnames(scATACseqCounts) = cellNames
weights = apply(scATACseqCounts + 0.001, 2, mean)
scATACseqCountsGapStat = getGapStat(scATACseqCounts, weights, nClusters = 1:30, nPerm = 30, nTop = 5000, quiet = FALSE)
It gets to 10% and then the error appears.
Thanks Zhixiang.
Timothy Daley
Stanford University, Departments of Statistics and Bioengineering.
________________________________
From: linzx06 <[email protected]>
Sent: Tuesday, August 21, 2018 5:15:29 PM
To: SUwonglab/scABC
Cc: Timothy Patrick Daley; Author
Subject: Re: [SUwonglab/scABC] error in gap statistic (#5)
Sure, please send it to me.
On Wed, Aug 22, 2018 at 7:30 AM, Timothy Daley ***@***.***> wrote:
Error in distMatrix[medoid, which(cluster == medoid)] :
subscript out of bounds
@linzx06 <https://github.com/linzx06> : do you know what this means? What
can I do to debug the issue? The data is from the Buenrostro hematopoietic
scATAC-seq data. I can send it to you if that'll help.
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<#5>, or mute the thread
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Hi guys, is this fixed? |
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Error in distMatrix[medoid, which(cluster == medoid)] :
subscript out of bounds
@linzx06 : do you know what this means? What can I do to debug the issue? The data is from the Buenrostro hematopoietic scATAC-seq data. I can send it to you if that'll help.
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