Additive Model For Microarray Fold Change
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Entering edit mode
13.3 years ago
Laurakat ▴ 50

Sadly the archives seem a bit bare on this topic...

Are there any software packages (preferably through R, but any open source package will work) that will perform fold-change calculations based on an additive model?

We are using microarray data from another study, so we only have normalized expression values (not the original CEL files). The goal is to relate genotype to expression values and a downstream tool requires that we have processed our data with an additive model. Previously we grouped homozygotes(AA, aa) together and disregarded heterozygotes then processed with lmfit through the LIMMA package in Bioconductor. However as far as I can tell there is no way to specify model with LIMMA. Is that correct?

Thank you so much for your help!

microarray bioconductor limma genotyping r • 3.1k views
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Are you fitting an additive model (e.g. evaluating the fit of a linear model specified by lm(expression~genotype) where genotype is coded {0,1,2} for the B allele frequency and evaluating the fit to the regression), or just calculating fold-change between samples of the specified genotypes?

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David-

If I understand your question correctly, you are asking whether we are grouping based on snp (i.e. all individuals regardless of genotype) or grouping by genotype (all homozygous dominant together, etc). We want to do the former. So for all snps we want to adjust the expression values to an additive model based on the the B allele frequency. If it helps, we are starting with the raw files from plink following a --recodeA transformation.

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13.2 years ago

Have a look at Vince Carey's GGTools package from Bioconductor. The paper is a bit dated and very significant changes and improvements have been made since its publication.

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Sean- Thanks for that resource. Looking at the bioconductor documentation, I am not immediately seeing a method to perform the desired analysis. Though we all know how sparse documentation can be! I will play around with the program and see what falls out. Thanks again!

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Entering edit mode
13.2 years ago
Laurakat ▴ 50

Unfortunately Sean's suggestion of CGTools didn't end up working out. Ultimately we did it by hand using the standard lm() function and some manual manipulation.

Thank you so much for your help!

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