Question

cmdscale() error: NA values not allowed in 'd', ask for help.

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Wagaa ▴ 10

@wagaa-23656

Last seen 4.5 years ago

United States

I am learning scRNA-seq analysis by following the workflow. The link is here https://www.bioconductor.org/help/course-materials/2017/BioC2017/Day2/Workshops/singleCell/doc/workshop.html#introduction

I encountered an error at 2.6.2 Dimensionality reduction Step.

W <- colData(se)[, grepl("^W", colnames(colData(se)))]
W <- as.matrix(W)
d <- dist(W)
fit <- cmdscale(d, eig = TRUE, k = 2)

The error information: Error in cmdscale(d, eig = TRUE, k = 2) : NA values not allowed in 'd'

Anyone may help me? thank you.

cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq • 3.5k views

ADD COMMENT • link updated 4.4 years ago by davide risso ▴ 980 • written 4.5 years ago by Wagaa ▴ 10

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ADD REPLY • link 4.4 years ago pankajku6678 • 0

score 0 · Answer 1 · 2020-07-07

Hello,

the workflow you are following is quite old (~3 years ago) and since then several changes happened to the zinbwave package. One of them is that it now uses the SingleCellExperiment class which stores the reduced dimension matrix in the reducedDim slot.

If you update your code to the following, it should work.

W <- reducedDim(se, "zinbwave")
d <- dist(W)
fit <- cmdscale(d, eig = TRUE, k = 2)

Best, Davide