design matrix for dge

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1234anjalianjali1234 ▴ 30

@1234anjalianjali1234-10835

Last seen 4.6 years ago

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

limma • 908 views

ADD COMMENT • link updated 7.9 years ago by Gordon Smyth 50k • written 7.9 years ago by 1234anjalianjali1234 ▴ 30

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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 REPLY • link 7.9 years ago chris86 ▴ 420

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