Question: Expression data preprocess and normalization
0
gravatar for hkarakurt
3.8 years ago by
hkarakurt110
hkarakurt110 wrote:

Hello everyone, I am relatively new in this field and I have different expression data sets from GEO. I am working on downloading them to R, pre-process and analyze. I found many different methods like RMA but I am not sure which one should I use. I want to use a simple method to build a script for all data sets. The simples methods are these: http://jura.wi.mit.edu/bio/education/bioinfo2007/arrays/array_exercises_1R.html (in the middle of page) http://felixfan.github.io/RMA-Normalization-Microarray/

Are those methods enough for normalization and good to use? What other methods do you advice? Should I change my methods depending on my data sets? My datas are all from Illumina HiSeq 2500 platform. I think I should not use Affy package for this. Thank you.

rna-seq gse bioconductor R geo • 2.5k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by hkarakurt110
1

You are working with RNA-seq data and looking at methods for microarray data, which is not the same. Have a look at this workflow as your starting point: Bioconductor RNA-seq workflow: gene-level exploratory analysis and differential expression

ADD REPLYlink written 3.8 years ago by WouterDeCoster45k

Actually I am looking for normalization methods for Illumina HiSeq 2500 expression data. Do platforms change the normalization method?

ADD REPLYlink written 3.8 years ago by hkarakurt110

Illumina HiSeq 2500 expression data

So, that's RNA-seq, right?

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by WouterDeCoster45k

Yes that's a RNA-seq.

ADD REPLYlink written 3.8 years ago by hkarakurt110

Then the workflow linked above is okay, for sure for all Illumina RNA-seq, possibly for other short-read sequencers too.

ADD REPLYlink written 3.8 years ago by WouterDeCoster45k
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