[BioC] edgeR - 3-dimensional Multidimensional scaling

Wed Nov 27 22:42:57 CET 2013

Dear Mark,

thanks for your help. I followed your instructions and it worked great!

Paraskevas

--
Paraskevas Iatropoulos, MD
Geneticist
Clinical Research Centre for Rare Diseases “ALDO E CELE DACCO”
IRCCS - Mario Negri Institute for Pharmacological Research
Via G.B. Camozzi, 3
Ranica (BG) - Italy
e-mail: iatropoulos at marionegri.it

----- Messaggio originale -----
Da: "Mark Robinson" robinson at imls.uzh.ch>
A: "Paraskevas Iatropoulos" <paraskevas.iatropoulos at marionegri.it>
Cc: bioconductor at r-project.org
Inviato: Mercoledì, 27 novembre 2013 20:59:35
Oggetto: Re: [BioC] edgeR - 3-dimensional Multidimensional scaling

Dear Paraskevas,

Maybe all you need is to set 'ndim=3' in your call to plotMDS() ?

> However, the 2D plot obtained with cmdscale using the counts per million ( cpm ) is much different compared to that obtained with plotMDS .

Have a careful read of:

?plotMDS.DGEList
?plotMDS

In short, plotMDS() does something very different with a DGEList object than with a matrix of numbers.

Then, maybe try something like:

# Taken from the plotMDS.DGEList help page
     ngenes <- 1000
     nlib <- 6
     counts <- matrix(rnbinom(ngenes*nlib, size=1/10, mu=20),ngenes,nlib)
     rownames(counts) <- paste("Gene",1:ngenes)
     group <- gl(2,3,labels=c("Grp1","Grp2"))
     counts[1:200,group=="Grp2"] <- counts[1:200,group=="Grp2"] + 10
     y <- DGEList(counts,group=group)
     y <- calcNormFactors(y)

> mds <- plotMDS(y, top=200)
> mds$cmdscale.out
              [,1]        [,2]
Sample1  0.6296663  2.11210712
Sample2 -3.2338291 -0.68439921
Sample3  2.1070395  0.06385855
Sample4  0.2781657  0.60249359
Sample5  0.9806977 -3.12230808
Sample6 -0.7617402  1.02824803
> mds <- plotMDS(y, top=200, ndim=3)
> mds$cmdscale.out
              [,1]        [,2]       [,3]
Sample1  0.6296663  2.11210712 -1.3976172
Sample2 -3.2338291 -0.68439921  1.2745170
Sample3  2.1070395  0.06385855  2.8492196
Sample4  0.2781657  0.60249359 -0.4326530
Sample5  0.9806977 -3.12230808 -1.5085139
Sample6 -0.7617402  1.02824803 -0.7849524

Note, you don't *need* to set the 'top' parameter.  Then, just plot these in 3D.

Hope that helps.

Best, Mark

----------
Prof. Dr. Mark Robinson
Bioinformatics, Institute of Molecular Life Sciences
University of Zurich
http://tiny.cc/mrobin

On 27.11.2013, at 16:15, Paraskevas Iatropoulos <paraskevas.iatropoulos at marionegri.it> wrote:

> 
> Hi!
> 
> it would be of great help, if someone could suggest a solution to the following problem. I used edgeR to analyze RNA Seq expression data (3 different cell lineages with 2 biological replicates for each lineage). I used the plotMDS () function to get a 2D plot of multidimensional scaling. I was asked to perform a 3D plot but I am not able to find a solution
> 
> According to Cell 151:559–575, where they report to perform 3D- MDS , and a web guide (Quick-R) I used the cmdscale () function as follows:
> d <- dist( mydata ) # Calculate the euclidean distances between the rows
> fit <- cmdscale (d, eig =TRUE, k=3) # k is the number of dimensions
> x <- fit$points[,1]
> y <- fit$points[,2]
> z <- fit$points[,3]
> Then I use the scatterplot3D software to obtain the grafic in 2D or 3D.
> 
> However, the 2D plot obtained with cmdscale using the counts per million ( cpm ) is much different compared to that obtained with plotMDS . Moreover, the results with the above cmdscale procedure are strange from a biological point of view, so I suppose that I did something wrong. Since the dimensions in the edgeR graphic are "leading logFC ", I calculated the log2 fold-chage (log2 [ cpm of the replicate / average expression in all 6 samples]) and I get a 2D graphic very similar but not identical to edgeR . In this way I can also have a 3D plot.
> 
> I am not sure if it is right to use the log2-FC to get. Do you think it is ok ? Is there a way to perform a 3D-MDS with edgeR ? Can you suggest me a way to perform the 3D- MDS , please?
> 
> Thank you in advance.
> 
> Paraskevas
> 
> 
> 
> --
> Paraskevas Iatropoulos, MD
> Geneticist
> Clinical Research Centre for Rare Diseases “ALDO E CELE DACCO ”
> IRCCS - Mario Negri Institute for Pharmacological Research
> Via G.B. Camozzi , 3
> Ranica ( BG ) - Italy
> e-mail: iatropoulos @ marionegri .it
> 
> ----------
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L'IRCCS - Istituto di Ricerche Farmacologiche Mario Negri desidera ringraziare i 13.768 donatori, di cui non conosce i nomi, che nel 2011 hanno devoluto il loro 5 per mille a sostegno della nostra attività e assicurare loro che tutto quanto ricevuto sarà esclusivamente impiegato per le nostre ricerche. Siamo naturalmente molto grati a tutti coloro che anche quest'anno hanno deciso di rinnovare ancora la fiducia nel nostro lavoro con la destinazione del loro 5 per mille.

A coloro che stanno per farlo ricordiamo di firmare ed indicare il nostro codice fiscale

                         03254210150

nel riquadro "Finanziamento agli enti della ricerca scientifica e dell'università.

Per maggiori informazioni:

IRCCS - Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19 - 20156 Milano
Tel: +39 02 390141 - Fax: +39 02 3546277 +39 02 39001918
Internet: www.marionegri.it, mnegri at marionegri.it