RNAseq and microarray combined clustering
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4.7 years ago
miesmi ▴ 10

Hello

I have data from RNAseq and microarray and I want to make a HCA or PCA to determine grouping of data. I am wondering if anyone knows how I have to normalize rnaseq reads and microarray signals together.

Thaks in advance

RNA-Seq • 925 views
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In my opinion, it's worth trying (but be sure you have controls to assess whether clustering is due to rna-seq/microarray differences or biological differences).

Some ideas to reduce bias:

  • Try quantile-normalizing your datasets.
  • Try using MDS with non-parametric distance metrics (e.g. those based on spearman rather than pearson).

FYI, it's much easier to integrate microarray and rna-seq together when you compare downstream analyses (e.g. differential gene expression) rather than gene expression values.

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You should not, data is not quantified in the same way, therefore you will have a lot of bias.

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There are tools such as the R package MOFA which have been developed to tackle this problem of low-dimensional reduction of different -omic technologies and kind of find out which of the data better explain the observed variability and such.

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4.7 years ago
miesmi ▴ 10

Thanks to all,

after reading answers , I think that the better option will be calculate log fold changes in each plantform and then make correlation based analysis.

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