algorithm for cluster analysis of illumina microarray data

Question

[Kritika]

Hi everyone

I want to know for cluster analysis of illumina microarray gene expression data (in idat format) which all the algorithms are used and which software are available ?

What i know is BHC from bioconductor can be used but i am not sure

any help?

Thanks!!!!!!!!!!!

Answer 1

[GouthamAtla]

cluster3.0 and java Treeview may help you. Here is a small guide:

Regarding algorithm, It depends on what you want to achieve. If you are just interested to look how the samples group together, hierarchical clustering will be a good choice and widely used to show clustering of samples.

Here is a good notes.

P.S: Instead of searching for a clustering program that deals with idat format, I would first convert them to text files. Then you have more control over what do you want to do.

[Kritika]

Thanks for it other then that is lumi bioconductor package which can do it by hierarchical clustering between genes only problem is it will accept .txt file which is generated by genomestudio.

Any other help will be appreciated

[Kritika]

the software which you said is also taking txt file which is obtained from genome studio i am asking with idat files

[GouthamAtla]

There must be some tools to parse idat files and gives the data in text format. I edited my answer.