Question

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

0

Entering edit mode

Wagaa ▴ 10

@wagaa-23656

Last seen 3.9 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 • 3.1k views

ADD COMMENT • link updated 3.8 years ago by davide risso ▴ 950 • written 3.9 years ago by Wagaa ▴ 10

0

Entering edit mode

WonderMouse Technologies is web designing company, which provides web designing services in Dubai. The company provides cost-competitive website design and development solutions to start-ups, SME’s and enterprises. Our well-organized, flexible and transparent processes help us create Web Design Services or solutions that meet client’s present as well as future demands. The expert professionals of website design company in Delhi can meet all your requisites efficiently and as a mobile application development company in India, we focus on the goals, budget, and success of the businesses. Whether you are looking for best mobile app development services, desktop or web apps development services or web designing services, Wondermouse technologies is top destination for all your requirements. Our dedicated team of designers, developers use the best tools in order to ensure the best deliverables for every project.

ADD REPLY • link 3.8 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