Question: Public RNA-Seq and Microarray samples from same tissue
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gravatar for Ar
3.0 years ago by
Ar830
United States
Ar830 wrote:

I am looking for a public dataset that has RNA-Seq and Microarray samples from the same tissue &/ same conditions but I am interested in the RNA-Seq dataset that has batch effects. Can you please share the GEO id or Array Express link ?Thanks!

ADD COMMENTlink modified 19 months ago by Kevin Blighe42k • written 3.0 years ago by Ar830
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gravatar for Kevin Blighe
19 months ago by
Kevin Blighe42k
Republic of Ireland
Kevin Blighe42k wrote:

Researchers will not typically study batch effects directly if they have another end-point of interest, and may only make a loose reference to batch in supplementary methods. As such, it may be difficult to find the exact experimental set-up that you want.

However, you should be aware that the TCGA has expression data on various cancers as both RNA-seq and cDNA microarray, and, because it's the TCGA, most of these samples will overlap centers and therefore be from different batches. Take a look at the NCI's Genomic Data Commons to see what you can find.

Also take a look at these:

ADD COMMENTlink written 19 months ago by Kevin Blighe42k
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