I have a query regarding differential gene expression using limma-voom.
1
0
Entering edit mode
@28946033
Last seen 20 months ago
India

I used the following pipeline for RNA Seq Analysis Fastq-Trimmomatic- Hisat2(gtf file was annotated)-featurecounts After featurecounts I tried to do limmavoom, but I get error saying this

An error occurred with this dataset:
format html database dm3
[1] "Extracting counts"
[1] "Generating DGEList object"
[1] "Generating Design"
[1] "Calculating Normalisation Factors"
[1] "Generating Contrasts"
[1] "Generating MDS plot"
Error in plotMDS.default(y, top = top, labels = labels, pch = pch, cex = cex, :

KIndly help, I am not able to solve my problem, I will be highly thankful

RNASeqData DESeq2 • 681 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 9 minutes ago
WEHI, Melbourne, Australia

You would have to tell us what software interface you are using. This help forum is for people using R and Bioconductor packages directly. You seem to be using a non-Bioconductor interface to limma because the messages you show are not from limma or voom. You are obviously using the limma and edgeR packages but via some interface or script, and the error is coming from the interface.

I guess you are probably using the Galaxy interface, but there is no way for us to help you with that. You would need to contact the Galaxy help forums.

ADD COMMENT

Login before adding your answer.

Traffic: 853 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6