RNA seq gene expression data and clustering

[am_Abdullah]

I have some questions:

1. where can I find some RNA-seq gene expression data to download ?

2. I want to do some clustering and classification on RNA-seq gene expression data? from my reading I read that I should normalize the read count before input them to classification or clustering. Is it correct?

Thank you

[dpryan]

1. GEO, SRA, ENA, etc.
2. Likely, it depends on how your classifier works. You'll definitely want to normalize before clustering.

[am_Abdullah]

Is there any tutorial teach me how to search in these databases to find gene expression across different samples?

[diego diaz]

This is a good tutorial to perform differential expression analysis with Deseq2

http://dwheelerau.com/2014/02/17/how-to-use-deseq2-to-analyse-rnaseq-data/

Most popular programs to perform differential expression analysis are written in R, a programming language oriented to statistical analysis. If you aren't familiar with R, I recommend you learn

[GenoMax]

Is there any tutorial teach me how to search in these databases to find gene expression across different samples?

In general there is raw data in databases such as SRA, ENA etc. Some records may have summarized gene expression values but you can't search for those easily. You will need to get the sequence data and do the analysis yourself following a tutorial such as the one Diego posted or referring to this vignette: http://www.bioconductor.org/packages...doc/DESeq2.pdf

If you are only interested in browsing expression levels (without doing any analysis) then ArrayExpress may help: http://www.ebi.ac.uk/arrayexpress/browse.html

[Michael Love]

Another pointer: our DESeq2 tutorial for people just starting with RNA-seq is here:

http://bioconductor.org/help/workflows/rnaseqGene/

[maxsalm]

This is also a great tutorial: http://arxiv.org/abs/1302.3685