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Old 11-01-2012, 05:14 AM   #1
seeker
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Default edgeR MDS plot: any way to get genes contributing to axes out?

Hi All,

I'm working with edgeR and have a MDS plot that is interesting but want to know which genes contribute to the two axes. Any suggestions of how to get this out?

Cheers!
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Old 01-07-2015, 01:12 PM   #2
MBWatson
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Hello! I am also interested in determining which genes contribute to the axes in my MDS plot. Did you ever find a way to do this? Thank you!
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Old 01-07-2015, 02:08 PM   #3
seeker
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No, I'm afraid I never figured it out. Perhaps this will spur others who might know how to share.
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Old 01-09-2015, 11:05 AM   #4
dariober
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Hi- I think you want to look at the rotations (or loadings) from a Principal Components Analysis (MDS is PCA where the data are a distance matrix).

Let's see this example... You have 10 samples and 23 genes. Gene A and B are anticorrelated while C is highly expressed in samples 4, 5, 6, and 7. The remaining 20 genes do not show any pattern of expression:

Code:
n<- 10
A<- 1:n
B<- c(1, 1, 1, 10, 10, 10, 10, 2, 2, 2)
C<- n:1
k<- matrix(rnorm(n= 20 * n, mean= 5, sd= 0.5), ncol= n)
dat<- as.matrix(rbind(A, B, C, k))
rownames(dat)<- LETTERS[1:nrow(dat)]

round(dat)
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A    1    2    3    4    5    6    7    8    9    10
B    1    1    1   10   10   10   10    2    2     2
C   10    9    8    7    6    5    4    3    2     1
D    5    5    5    5    5    6    4    5    5     5
E    5    5    5    5    5    6    6    5    4     5
...
If you do a PCA and plot you see that the 10 samples form 3 groups, as expected:

Code:
pc<- prcomp(t(dat))
plot(pc$x)

# Or also:
biplot(pc)
For question "Which genes contribute to the separation", let's have a look at the rotations:

Code:
round(pc$rotation[1:10,1:2], 3)
     PC1    PC2
A  0.408 -0.567
B  0.797  0.581
C -0.408  0.567
D  0.068  0.031
E  0.009 -0.018
F -0.009 -0.006
G  0.008 -0.042
H -0.030 -0.014
I -0.048  0.014
J -0.009  0.015
...
We can see that A, B, C contribute the most to the variation.

(For this questions you might get better answers on the Bioconductor mailing list...)

Hope this helps (and make sure I'm not missing anything...)
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Old 01-12-2015, 05:16 AM   #5
seeker
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Thanks for that. I was also sent this link which explains why they do not provide this information.

https://support.bioconductor.org/p/57328/#57340
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differential expression, edger, mds, pca, rna-seq

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