Differential expression analysis with LIMMA results
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27 days ago
najioumayma ▴ 10

Hello,

I did a differential expression analysis of RNA seq data (normalized RSEM) from TCGA with VOOM and another time with Limma trend , but i got as result most of the genes with positive log2 fold change and significant p-value. Do you have any idea about this issue ?

this is the figure of my volcano plot :

Volcano plot

DGE • 149 views
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Can you show an MA-plot (AveExpr on x-axis, and logFC on y)? What are the samples, so what are the groups?

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thanks for the reply , so for the groups : we have 2 groups high and low of a gene and samples are patients.

I don't have an MA-plot i just did a volcano plot.

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this an example of the results tab

voom results

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