Question: algorithm for cluster analysis of illumina microarray data
0
gravatar for Kritika
3.5 years ago by
Kritika260
India
Kritika260 wrote:

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!!!!!!!!!!!

microarray ilumina cluster • 986 views
ADD COMMENTlink modified 3.5 years ago by geek_y9.8k • written 3.5 years ago by Kritika260
0
gravatar for geek_y
3.5 years ago by
geek_y9.8k
Barcelona
geek_y9.8k wrote:

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.

ADD COMMENTlink modified 11 months ago by RamRS23k • written 3.5 years ago by geek_y9.8k

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

any other help will be appreciated

ADD REPLYlink written 3.5 years ago by Kritika260

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

ADD REPLYlink written 3.5 years ago by Kritika260

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

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by geek_y9.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1323 users visited in the last hour