Question: Comparing DEG result from different experiment
1
gravatar for bharata1803
2.9 years ago by
bharata1803470
Japan
bharata1803470 wrote:

Hello all,

So I have a simple question. Suppose I download 2 or more dataset from NCBI GEO. Those dataset come from different experiment especially the NGS machine. For example one of them use Illumina and others use Ion Torrent.

My first question is, if I calculated each dataset separately for DEG, using EdgeR, Limma/Voom, or DEseq2, are these log fold change comparable?

For example, Dataset 1 comes from Illumina Hiseq and I have logfoldchange from DESeq2. ANother Dataset 2 comes from IonTorrent and I have logfoldchange from DESeq2.

My second question is, what if I calculate the DEG using different method? One of them using DESeq2 and other use Limma/voom?

What should I consider?

Thank you.

deg rna-seq • 1.2k views
ADD COMMENTlink written 2.9 years ago by bharata1803470
1

If they are properly normalized and are the same comparisons on the same biological and experimental background yes. Different methods should agree on the magnitude of the change if not in the value itself, apply common sense.

ADD REPLYlink written 2.9 years ago by LluĂ­s R.970

Thank you, I just want to make sure it is make sense. I have several times compare DEG analysis using DESeq2 and Limma and edgeR with same dataset and they produce similar result.

ADD REPLYlink written 2.9 years ago by bharata1803470

The literature might be helpful:

ADD REPLYlink written 2.9 years ago by Sean Davis26k
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