Question: MIcroarray data analysis?
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gravatar for mathavanbioinfo
3.7 years ago by
India
mathavanbioinfo50 wrote:

Hi Can we combine or correlate the results of NGS and Microarray data? In the results of GEO2R some of the value are missing? How i treat that probe id?

next-gen • 1.1k views
ADD COMMENTlink modified 3.7 years ago by Charles Warden7.4k • written 3.7 years ago by mathavanbioinfo50

You can use missing value imputation. impute package form bioconductor

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Tanvir Ahamed 290
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gravatar for Charles Warden
3.7 years ago by
Charles Warden7.4k
Duarte, CA
Charles Warden7.4k wrote:

You should rename your question and/or ask two separate questions.

I've found that it is possible to compare microarray and RNA-Seq gene expression values by comparing the expression of one set of genes relative to another set of genes (in the links below, TCGA is RNA-Seq while all other datasets are microarrays).

https://peerj.com/articles/159/#table-3 https://peerj.com/articles/159/#fig-3

In general, the absolute values won't be comparable (and I wouldn't recommend doing anything like quantile normalization to make them similar), and the fold-change values for individual genes will probably also be different (although you could do independent analysis and look for overlapping genes).

ADD COMMENTlink written 3.7 years ago by Charles Warden7.4k
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