Question: microarray data analysis
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gravatar for me.sr1510
2.4 years ago by
me.sr15100
me.sr15100 wrote:

Hello everyone My doubt is that can we compare the analysis result of different platforms of microarray. I have done d analysis using the GEO.2R the result file contains the pvalue log2FC and gene name. These columns are extracted from the file. Similarly it is done for another study done of different platform. Can we compare the gene names obtained from two different study done on two different platform?

gene • 555 views
ADD COMMENTlink modified 2.4 years ago by russhh5.5k • written 2.4 years ago by me.sr15100

Please select a more descriptive title for your thread(s). "microarray data analysis" is far too general, you probably should go with something like "compare microarray data across different platforms".

ADD REPLYlink written 2.4 years ago by WouterDeCoster44k
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gravatar for rice.researcher
2.4 years ago by
Korea, Republic Of
rice.researcher150 wrote:

You can try Shiny app BatchQC. It can deal with multiple batches and eliminate batch effect.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by rice.researcher150
0
gravatar for JJ
2.4 years ago by
JJ520
JJ520 wrote:

See a similar discussion: What are the requirements to use data generated in other microarray experiments as a control?

ADD COMMENTlink written 2.4 years ago by JJ520
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gravatar for russhh
2.4 years ago by
russhh5.5k
UK, U. Glasgow
russhh5.5k wrote:

Yes, you can compare them. However, I would urge against doing fixed-effects metaanalysis since you shouldn't expect the fold-changes to be the same even if it was the same samples put on two different platforms (in my experience log-fold-changes tend to be extremely similar - even when paralogues are compared across species - for a well designed experiment).

What you could do is define two genesets using the upregd genes and the downregd genes from one dataset and look at the distribution of fold-changes, or p-value ranks for these genesets in the other dataset by GSEA

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by russhh5.5k
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