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Question: design matrix for dge
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gravatar for 1234anjalianjali1234
17 months ago by
1234anjalianjali12340 wrote:

I am doing Cross-platform normalization and network-based data analysis of gene expression data to find out potential biomarker of cancer .I have merged 3 datasets without any treatment ( two of Affymetrix Human Genome U133A Array and one with Affymetrix Human Genome U133A Array plus 2, platform GPL96 AND GPL570) using insilicomerging package. I have 229 cancer samples and 74 normal one with i.e a ratio of about 3:1. I want to do the linear model analysis to find out differentially expressed genes.

please someone help me

ADD COMMENTlink modified 17 months ago by Gordon Smyth32k • written 17 months ago by 1234anjalianjali12340

If you want to do standard differential expression I would refer you to the limma manual https://www.bioconductor.org/packages/3.3/bioc/vignettes/limma/inst/doc/usersguide.pdf.

ADD REPLYlink written 17 months ago by chris86320
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