Question: Comparison Between Independently-Derived Microarray Datasets?
3
gravatar for Johnny R
7.3 years ago by
Johnny R50
Johnny R50 wrote:

I've gotten a number of microarray datasets from GEO and arrayexpress, each of which looks at similar chemical treatments of mammalian cells. I downloaded the processed data, and from this I can easily generate log2 fold change values for each probe between the treated sample and the untreated sample. Are there any caveats to comparing these log2 FC values between datasets? Is this type of analysis OK, or do I need to go back to the CEL files for each dataset and normalize everything in one particular way?

geo comparison microarray • 1.9k views
ADD COMMENTlink written 7.3 years ago by Johnny R50

Johnny,

Can you provide me an example of your code, I want to know how you was reading the processed data and how you was generating the log2 FC for probes. Thanks

 

ADD REPLYlink written 3.6 years ago by Bioinformatist Newbie230
4
gravatar for Neilfws
7.3 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Normalizing CEL files from different studies is fraught with statistical problems.

What you want to perform is a meta-analysis. Try searching this site for that term with respect to microarrays - there have been several previous questions on the topic. If you're using Bioconductor, take a look at the RankProd package for a good introduction to the topic.

ADD COMMENTlink written 7.3 years ago by Neilfws48k

thanks, that looks like a useful package to add to the arsenal.

ADD REPLYlink written 7.3 years ago by brentp22k
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