Hi everybody!

The question is 

1. Take a closer look at gene FBgn0039186. This gene shows significant differential expression (at Padj<0.05) in the two-factorial analysis but not the unifactorial analysis. What could explain this difference? 

First I did unifactorial and two factorial analysis seperately and know I have to explain why they have difference padj in this gene

Codes:

Unifactorial analysis: 

resgene <- results(ddsmain['FBgn0039186']) 

padj is 0.32227

Codes for the two-unifactorial analysis:

resgenenew <- results(ddsnew['FBgn0039186'])

padj is 0.0023

Does anybody know why it is so?

Thank u in advance

Hira

This looks like a question from a workflow or instructional material.

Without any of the prelude or context, it's not possible to answer your question. 

The Bioconductor support forum is really designed for asking software related questions that aren't answerable by the package manual pages or vignette.