Open timydaley opened 6 years ago
Sure, please send it to me.
On Wed, Aug 22, 2018 at 7:30 AM, Timothy Daley notifications@github.com 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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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 notifications@github.com 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 notifications@github.com 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.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/SUwonglab/scABC/issues/5, or mute the thread https://github.com/notifications/unsubscribe-auth/ALQrSYU8Q9W3_InN3ssSqOcEAqHBTYUjks5uTJgjgaJpZM4WGwTU .
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Hi guys, is this fixed?
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.