I have a query regarding differential gene expression using limma-voom.
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@28946033
Last seen 8 weeks 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 • 120 views
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@gordon-smyth
Last seen 1 hour 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.

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