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Forum: RNA Sequencing 03-07-2016, 06:45 AM
Replies: 3
Views: 2,323
Posted By vilperte
Hi, No, I didn't get any feedback. What...


No, I didn't get any feedback.

What I did was to extracted the geneset of my interest from CummeRbund and plot the PCAs using the ade4 package. It is also a very easy package to work with....
Forum: RNA Sequencing 01-12-2016, 03:13 AM
Replies: 3
Views: 2,323
Posted By vilperte
CummeRbund - PCA


I'm using the PCA plot function implemented in the CummeRbund package. The package is very user-friendly, however, I can't find a way to get the eigenvalues or the percentage of each...
Forum: Bioinformatics 07-10-2015, 04:56 AM
Replies: 0
Views: 2,037
Posted By vilperte
PCA plot in cummeRbund with subset genes

Hello all,

I'm trying to create a PCA plot with my data. I managed to create it with all my genes using the standard script:

genes.PCA<-PCAplot(genes(cuff), "PC1","PC2")

However, I would...
Forum: Bioinformatics 04-14-2015, 10:50 AM
Replies: 1
Views: 855
Posted By vilperte
Getting FASTA collapsed reads


I need to convert an uncollapsed FASTA file in a collapsed one.

I managed to do that using a script from the miR-PREFeR tool for miRNA prediction. However, I need them to look like this:...
Forum: Bioinformatics 04-14-2015, 10:42 AM
Replies: 2
Views: 1,910
Posted By vilperte
Error in MIREAP


I'm trying to run MIREAP to predict novel miRNAs in my dataset.
However, when I run the script, the following message appears:

Can't use an undefined value as an ARRAY reference at...
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