Question: Joint Preprocessing of RNA-Seq and Microarray datasets
1
gravatar for Jo
4.0 years ago by
Jo10
Jo10 wrote:

Hi,

I would like to jointly pre-process RNA-Seq datasets and Microarray datasets together. Are there any pipelines or ways to do this? Please advise.

Thanks

 

ADD COMMENTlink modified 4.0 years ago by Gordon Smyth39k • written 4.0 years ago by Jo10

That's going to depend very heavily on what you want to do with this data.

ADD REPLYlink written 4.0 years ago by Ryan C. Thompson7.4k

I want to normalize, remove batch effects (ComBat), and run limma on the datasets jointly.

ADD REPLYlink written 4.0 years ago by Jo10
Answer: Joint Preprocessing of RNA-Seq and Microarray datasets
1
gravatar for Gordon Smyth
4.0 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

No, you can't preprocess RNA-seq and microarrays together, nor would I include them in the same linear model in limma. The technologies are just too different.

Edit: The way that we usually handle this is to analyze the RNA-seq and microarray studies separately, then relate one experiment to the other using gene set tests (roast, barcodeplot etc) or a scatterplot of genewise log-fold-changes (e.g., microarray on the x-axis vs RNA-seq on the y-axis).

None of this requires batch correction or meta analysis.

 

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Gordon Smyth39k

Thanks for the reply. Is it possible to do a meta-analyses combining RNA-Seq datasets and Microarray datasets? If so how? Thanks in advance.

ADD REPLYlink written 4.0 years ago by Jo10

Assuming that the RNA-Seq and microarray datasets are based on the same types of samples, the basic idea would be to process each separately, and then use something like the GeneMeta package to analyze.

ADD REPLYlink written 4.0 years ago by James W. MacDonald52k
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