Question

Calculate correlation matrix for gene expression data

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lvu2 • 0

@lvu2-12795

Last seen 7.0 years ago

Dear BioC,

I got mRNA gene expression (p-value and normalized expression level) of 623 genes from 12 samples.

I am very new to R and learning now. I am looking for helps to analysis our gene expression data:

1. Principal component analysis: between groups of samples

2. Gene expression correlation ( all to all)

Since I got R 3.3.3 run on R-studio, neither Biobase nor limma is compatible. It is greatly appreciated that if someone can help me with detailed scripts.

R > install.packages("Biobase")
Warning in install.packages : package ‘Biobase’ is not available (for R version 3.3.3)

Thank you so much for your helps.

Luan

R differential gene expression • 3.6k views

ADD COMMENT • link updated 7.0 years ago by sebastiano.curreli • 0 • written 7.0 years ago by lvu2 • 0

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install.packages won't work.

You can only install bioconductor packages using the biocLite function from the BiocInstaller package.

These instructions can be found on the Install page on the Bioconductor website, as well as the "Installation" section of each of the packages you are trying to install. For instance, take a look at the Installation section of the Biobase package.

ADD REPLY • link 7.0 years ago Steve Lianoglou ★ 13k

score 0 · Answer 1 · 2017-04-11

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Entering edit mode

sebastiano.curreli • 0

@sebastianocurreli-9937

Last seen 6.9 years ago

Hi Luan,

regarding your analysis I'd suggest you to check out the following R packages:

PCA-->FactoMineR: http://factominer.free.fr/classical-methods/principal-components-analysis.html

Correlation analysis-->rcorr: https://www.rdocumentation.org/packages/Hmisc/versions/4.0-2/topics/rcorr

ADD COMMENT • link 7.0 years ago sebastiano.curreli • 0