Question: Micoarray meta data analysis
0
gravatar for au.rinki.bio
4 months ago by
au.rinki.bio10
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 4 months ago by guangyan.zh00 • written 4 months ago by au.rinki.bio10

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

ADD REPLYlink written 4 months ago by WouterDeCoster38k

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

ADD REPLYlink written 4 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 4 months ago by Kevin Blighe41k
0
gravatar for guangyan.zh0
4 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 4 months ago by guangyan.zh00
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1790 users visited in the last hour