[BioC] plotMDS error

[Wu, Di]

Hi Nicolas,

What is your input "cds"?

The input should be matrix, or "any data object which can be coerced to a matrix, such as ExpressionSet or EList".

Di


----
Di Wu
Postdoctoral fellow
Harvard University, Statistics Department
Harvard Medical School
Science Center, 1 Oxford Street, Cambridge, MA 02138-2901 USA

________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Nicolas Devos [nicolasdevos at mac.com]
Sent: Wednesday, November 14, 2012 5:37 PM
To: bioconductor at r-project.org
Subject: [BioC] plotMDS error

Hi,

I ve been trying to use edgeR for RNA-Seq Dierential Expression and I am trying to use in R the plotMDS function but I get the following cryptic error message

> plotMDS( cds , main = "MDS Plot for Count Data", labels = colnames( cds$counts ))
Error in cmdscale(as.dist(dd), k = ndim) :
  'k' must be in {1, 2, ..  n - 1}

Would any of you have an idea what this error  mean.

Thanks for your help

Best regards

Nicolas





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