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Questions tagged [mds]

Questions regarding MDS - Multidimensional Scaling R functions

101 questions
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PCA or MDS for groups in R

I have a data matrix which has specific columns and row-groups. Promoters Exons Introns Intergenic UTR5 UTR3 EncodeDnase TFBS CpGislands CpGshores CpGshelf Enhancer Valley umrs canyons genebodies enhancer34 groups 44905 34778 49182 32420…
user44552
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Python: Can I take a manifold object as a model

I have a group of high-dimensional (250 dimensions) data. To get rid of unnecessary dimensions and to easily visualize data on a figure, I used class sklearn.manifold.MDS and its method fit_transform(data) and already got the transformed data in…
gladys0313
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How to use Master Data Services data then? The MDS lifecycle

So I know that we need to create Master Data Services db to make data clean, right, consistent, etc. We can import some data there, then process it.. and then? We should then export it to another db, is it so? So MDS is like a set of tools to clean…
Lisa Aaron
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R Vegan: evaluate pairwise permanova significance between comparisons

I'm looking for a statistical test that will allow me to evaluate whether pairwise comparisons are statistically different from one another. I'm using ecological community count (abundance) data sampled across multiple sites before, during, and…
Joshua Smith
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failure to converge after 300 iterations. Last change (0.1382513330677284) was greater than tolerance (0.001)

I'm using MDS in julia. 'Here is my code D = pairwise(Euclidean(), mat_new) M = fit(MetricMDS, D; distances=true, maxoutdim=2, metric=isotonic) And I got error saying failure to converge after 300 iterations. Last change (0.1382513330677284) was…
Joe
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differentiate MDS and PCA in Julia

I'm using both MDS and PCA in the package MultivariateStats.jl. My code is M = fit(PCA, matrix; maxoutdim=2) Yte = predict(M, matrix) M1 = fit(MDS, matrix; maxoutdim=2, distances=false) Yte1 = predict(M1) Soon I found that Yte and Yte1 are always…
Joe
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ceph fs mds stuck in `up:rejoin` state - `failed to open ino 0x101 err -116/0`

Ceph stuck in case of disk full, but after fixing, the cephfs mds stuck in rejoin state for a long time. Ceph -s truncated output: cluster: id: (deleted) health: HEALTH_WARN 1 filesystem is degraded services: mon: 6…
zitsen
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MDS gets hung when computing on large matrix

I am trying to preform dimension reduction to 2 dimensions from a 64535 x 67 matrix to a 64535 x 2 matrix. I am not sure what the reasons are for why the fit transform calculation below is getting hung besides the fact this is a large matrix and a…
cap
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Multi-dimensional scaling for a very large dataset in R

I'm fairly new to R and I'm looking to nicely visualise my k-means segmentation of 368k customers with 36 variables into the 6 segments. To do this I believe I need to MDS the dataset before I can plot it but I always seem to encounter the same…
MarkA
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delete species names and arrows from ggord NMDS plot

I used ggord to create NMDS plot in R. It shows both plots and species together, but I want to remove all species names and arrows as well from the plot. Any solution? Here is my code: ggord(spherblr.nmds, envherblr$ecoutil, cols=c("red",…
N T
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Color the individuals of a R PCoA plot by groups

Should be a simple question, but I haven't found exactly how to do it so far. I have a matrix as follow: sample var1 var2 var3 etc. 1 5 7 3 1 2 0 1 6 8 3 7 6 8 9 4 5 3 2 4 I performed a…
Seb Matamoros
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create a changeset during staging ETL to Microsoft MDS for approval

In MDS, if i manually make changes, I can create a changeset for approval. Is there a way to force approvals for changes that come in via the staging tables? if so, How? thanks
arcee123
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How to plot an nmds with coloured/symbol points based on SIMPROF

Hi so i am trying to plot my nmds of a assemblage data which is in a bray-curtis dissimilarity matrix in R. I have been able to apply ordielipse(),ordihull() and even change the colours based on group factors created by cutree() of a hclst() e.g…
Lmm
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MDS business rule on more then one domain based attribute

I'm stuck with this problem on Master Data Service (MDS). I have an entity that has two domain based to other two entities. I created the first business rule with the first domain based and it works perfectly. But when I try to create a second…
Enrico Silvano
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Cross reference data between two entities in Master Data Service (MDS)

I am doing a POC in MDS wherein i have two tables in two different systems like below: A | B | C ----|-----|---- A1 | B1 | C1 A2 | B2 | C2 A3 | B3 | C3 and X | Y | Z ----|-----|---- X1 | Y1 | Z1 X2 | Y2 | Z2 X3 | Y3 |…
Json Brent
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