Question: Temporal Differential Expression Analysis Of Rna-Seq
gravatar for sychensau
6.5 years ago by
sychensau10 wrote:

In our present study, we experimentally induced and collected 45 samples showing a wide range of clinical signs of digestive disorders, including the complete healthy, slight, mild, and severe individuals. However, it is actually hard to definitely classify them into different groups. The trouble appeared when I tried to detect the differential expression gene based on comprehensive RNA-seq for these samples; mostly because there was no clear definition of categorical groups/conditions as wildly adopted in classical RNA-seq analyses. Even when these individuals were carefully grouped, it is also reasonable that the total variance within group would be very high because these members are not strictly comparable to the general biological replicates. Therefore, my inquiry is that whether there is an appropriate statistical method or tool to detect the gene expression significantly associated with the continuous biological changes rather than the clear categorical groups, especially for RNA-seq.

ADD COMMENTlink modified 6.2 years ago by Biostar ♦♦ 20 • written 6.5 years ago by sychensau10
gravatar for Mikael Huss
6.5 years ago by
Mikael Huss4.7k
Mikael Huss4.7k wrote:

I have used SAMSeq (paper) from the samr R package for this kind of analysis. There, you can specify a continuous target value using the "resp.type" parameter.

ADD COMMENTlink written 6.5 years ago by Mikael Huss4.7k

Thanks for you suggestion very much, I will try it.

ADD REPLYlink written 6.5 years ago by sychensau10
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