affymetrix microarray gene expression analysis

Question

[payaljain89]

I have microarray tumour data from TCGA db, now i have to do its differential gene expression analysis.Please suggest me freely available pipeline tools and required data to analyse it in R?

Answer 1

[Devon Ryan]

limma and affy would seem like a good match.

Answer 2

[akhilesh.mishra88]

hi, if you are using Affymetrix platform only then why not you use expression console and transcriptome analysis console software, it will make your life easier...with good reliable result.

Answer 3

[fatima]

Hi

affy and lima compatible with CEL file or any other format that we dl from TCGA relate to gene level 1 expression data of CODA and be text format

tnx