Regression Analysis between RNA-seq data and expression measured from ELISA
0
0
Entering edit mode
hrishi27n ▴ 20
@hrishi27n-11821
Last seen 3 months ago
United States

am trying to run a regression analysis on RNA-seq expected counts generated using RSEM. To perform the analysis I performed TMM normalization and extracted CPM values. I then used voomWithQualityWeights, lmFit and eBayes to perform association analysis. Since RNA has a different data distribution than the ELISA values, I would like to know if the steps that I followed are correct. I appreciate all your help and suggestions.

Following is my code:

d <- DGEList(counts=data, group=groups)
TMM <- calcNormFactors(d, method="TMM")
logCPM <- cpm(TMM, log=TRUE)

design <- model.matrix(~LN_AB, data=Pheno)
voom <- voomWithQualityWeights(data, design=design, lib.size=NULL, normalize.method="none")
fit1 <- lmFit(normalizeddata,design)
fit2 <- eBayes(fit1)
newFrame <- topTableF(fit2)

print(newFrame)

limma edger • 211 views
ADD COMMENT
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 355 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6