
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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