How to compare multiple microarray samples of small RNA expression from myeloid tissue with small RNA-seq

Question

[Saad Khan]

Hi I have a microRNA expression data from a cancer patient's myeloid cells (no replicate) . I want to do a one to many comparison using it against normals cells. Unfortunately there is no data available for smRNA-seq in GEO but there are quite a few data sets with microarray expression for myeloid cells. I was wondering if some one has already compared or tried to compare RNA-seq with microarray and what could be a valid approach to do so.

Answer 1

[mark.ziemann]

This type of data integration meta-analysis has been discussed a few times before.

• How To Go About Comparing Rnaseq With Micro Array Expression Data?
• Exon Arrays Vs Rna-Seq

I would suggest 2 other strategies. Easy one is to generate gene sets of significant genes from one experiment and then use GSEA (preranked) to see if those collections of genes are consistent between experiments.

The other more complicated one is to merge the DGE datasets on gene accession number and then perform a spearman correlation analysis based on the signed p-values (http://nar.oxfordjournals.org/content/38/17/e169.long).