Differential expression analysis with LIMMA results

Question

[leticia]

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 :

[ATpoint]

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

[leticia]

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.

[leticia]

this an example of the results tab