This is a test version of Biostars. For the public version, visit https://www.biostars.org.
MIcroarray data analysis?

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
• 2,351 views • link
updated by Charles Warden Charles Warden • written by mathavanbioinfo mathavanbioinfo

You can use missing value imputation. impute package form bioconductor

• 0 views • link
written by Tanvir Ahamed Tanvir Ahamed

1 answer

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).

• 0 views • link
written by Charles Warden Charles Warden

Log in to answer this question.

More posts like this