Question: Micoarray meta data analysis
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gravatar for au.rinki.bio
11 months ago by
au.rinki.bio10
University of Allahabad, India
au.rinki.bio10 wrote:

hello, I am working on a meta-analysis of the microarray data for the different type of cancer and trying to find out common genes for these cancers. For the same type of cancer (high grade) from different data sets, we get a different number of genes, as we increase the number of data sets, the common genes among these data sets were reduced. why this is occurring? If the different experiment gives the different results. how much the accuracy of these experiments?

ADD COMMENTlink modified 11 months ago by guangyan.zh00 • written 11 months ago by au.rinki.bio10

Don't you expect different results as you are working on multiple cancer types?

ADD REPLYlink written 11 months ago by WouterDeCoster42k

here, I am asking for same cancer (cervical) but datasets are different.

ADD REPLYlink written 11 months ago by au.rinki.bio10
1

Reproducibility is a constant issue in biomedical research. You should never expect that 2 studies looking at the same cancer sub-type will produce the same results. There are so many factors going into these experiments, many of which will never be reported - these factors are responsible for biases.

When you are analysing each dataset independently, you can then perform a 'meta analysis' of the results using RankProd.

ADD REPLYlink written 11 months ago by Kevin Blighe51k
0
gravatar for guangyan.zh0
11 months ago by
guangyan.zh00 wrote:

You should try gene-set level meta-analysis, it will be less affected by the small number of common genes shared across datasets.

ADD COMMENTlink written 11 months ago by guangyan.zh00
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