User: simarsidhu25

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Posts by simarsidhu25

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Comment: C: design for edgeR
... Thank you very much for your suggestions. ...
written 2.6 years ago by simarsidhu250
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Comment: C: design for edgeR
... Thanks. When I am doing this contrast  con <- makeContrasts(GroupR_TreatmentV - GroupS_TreatmentV, levels=design) -1    20 0  49814 1     32 then I am getting only these genes. ...
written 2.6 years ago by simarsidhu250
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Comment: C: design for edgeR
... I have another question. As I am using different contrasts and getting following results:  con <- makeContrasts(GroupR_TreatmentM, levels=design) -1  5809 0  37894 1   6163 con <- makeContrasts(GroupS_TreatmentM, levels=design) -1  5527 0  38098 1   6241 Identical DE genes in R and ...
written 2.6 years ago by simarsidhu250
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Comment: C: design for edgeR
... If I want to compare effect of treatment on only R group then I have used con <- makeContrasts(GroupR_TreatmentM, levels=design) am I right? Thanks. ...
written 2.8 years ago by simarsidhu250
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Comment: C: design for edgeR
... Thank you so much. It really helps a lot.     ...
written 2.8 years ago by simarsidhu250
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Comment: C: design for edgeR
... I have made the design matrix as well as contrast as suggested by you and find the DE genes in GroupR_TreatmentM - GroupS_TreatmentM: > y<-estimateDisp(y,design,robust=TRUE) > fit <- glmFit(y, design,robust=TRUE) > summary(fit$df.prior) > lrt <- glmLRT(fit, contrast=con) # To f ...
written 2.8 years ago by simarsidhu250
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Comment: C: design for edgeR
... I am doing separately and then comparing the genes of both the analysis. ...
written 2.8 years ago by simarsidhu250
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Comment: C: design for edgeR
... Thank you so much. I have tried it. But still I am getting the same genes in both GroupR_TreatmentM - GroupS_TreatmentM and GroupR_TreatmentV - GroupS_TreatmentV and expression of these genes are opposite in these contrasts. That means the genes which shows upregulation in one shows downregulation ...
written 2.8 years ago by simarsidhu250
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Comment: C: design for edgeR
... Group is R,R,R,R,R,R,R,R,R,R,S,S,S,S,S,S,S,S,S,S Treatment is V,M,V,M,V,M,V,M,V,M,V,M,V,M,V,M,V,M,V,M I want to compare effect of treatment in groupR vs groupS ...
written 2.8 years ago by simarsidhu250
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Comment: C: design for edgeR
... Group is the two types of plant lines like: resistant and susceptible. Plant is like: 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10 Same plant one is treated and another is not.   ...
written 2.8 years ago by simarsidhu250

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Can we use glmQLFit instead of glmFit and then glmLRT in edgeR

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