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Question: workflow for combining multiple microarray studies of same platform
1
gravatar for CHANG
5.2 years ago by
CHANG • 40
United States
CHANG • 40 wrote:

I am pooling together tumor samples of of 4 different histology from 4 GEO studies that are done on Affymetrix U133 Plus 2.0. I want to compare differential genes and  between each tumor histology and blood.  

Sample Tally  

study tumor_histo_1 tumor_histo_2 tumor_histo_3 tumor_histo_3 normal blood
GSE1 5 5     10 
GSE2 5 5     5
GSE3     10    
GSE4       10 5

Here are my proposed approaches  

1. Use insilicoDB to get fRMA normalized expression sets for each study so that all study will have been normalized the same way (Description: http://bit.ly/1OMmRJx). Use COMBAT to remove batch effects. Then run limma to get DE genes for each tumor histology against the pooled blood data.  

2. Pool together raw cell files from all studies, run RMA ,  then limma to get DE genes for each tumor histology against pooled blood.  

Thank you very much!
microarray • 1.6k views
ADD COMMENT • link •
modified 5.2 years ago • written 5.2 years ago by CHANG • 40
0
gravatar for Sean Davis
5.2 years ago by
Sean Davis ♦ 26k
National Institutes of Health, Bethesda, MD
Sean Davis ♦ 26k wrote:

fRMA probably offers some advantages over straight RMA, particularly if you are planning to add more samples/studies down the road. That said, the batch effects are confounded with your variable of interest  (tumor histology), so your results will just need to be interpreted carefully.
ADD COMMENT • link written 5.2 years ago by Sean Davis ♦ 26k

What about pooling all the raw cell files from studies and run fRMA, is there any advantage of doing that over fRMA on individual studies then run COMBAT?

ADD REPLY • link written 5.2 years ago by CHANG • 40
0
gravatar for CHANG
5.2 years ago by
CHANG • 40
United States
CHANG • 40 wrote:

Thank you in advance.
ADD COMMENT • link modified 5.2 years ago • written 5.2 years ago by CHANG • 40

Hi Chang

I am keen to combine multiple GEO datasets (all run on Affymetrix U133 plus 2.0) and came across your thread. I was wondering what approach you ended up using in order to combine your datasets? I would appreciate any help.

Thanks

ADD REPLY • link written 4.0 years ago by bcbio_uk • 0
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