User: prathap1708

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Posts by prathap1708

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Comment: C: Contrasts & coefficients in limma
... Thanks prof. The two DGE list objects are same but we removed genes which were expressed very low in the 2nd DGE object.   ...
written 21 months ago by prathap17080
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Comment: C: Contrasts & coefficients in limma
...  I did linear modeling fitting and then the contrast was done.I didn't post the last few lines of code in the previous question. Sorry for that. Please see the remaining code here. Thanks for your spontaneous reply. # Usual limma pipeline vfit <- lmFit(v, design.adipose) vfitAdipose <- contra ...
written 21 months ago by prathap17080
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Comment: C: Limma voom RNA-seq analysis with both categorical and continuous confounders
... Ok. I'm going to use removeBatchEffect() to retrieve data which will be adjusted for confounders like gender, age and control gene expression. Could it make sense? ...
written 21 months ago by prathap17080
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Comment: C: Limma voom RNA-seq analysis with both categorical and continuous confounders
... Thanks gordon. I will post as new question. ...
written 21 months ago by prathap17080
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Contrasts & coefficients in limma
... Hi, I have a doubt regarding contrasts. In my case, i understood,the 1st coefficient is comparison of MHO with MHNW, 2nd coefficient is comparison of MAO with MHNW and 3rd coefficient is comparison of MAO with MHW . Please let me know, if I understood wrong. Please find my code below. design.adip ...
design and contrast matrix written 21 months ago by prathap17080 • updated 21 months ago by Gordon Smyth38k
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Comment: C: Limma RNA seq analysis_VOOM
... Thanks for that. In removeBatchEffects function, removeBatchEffect(x, batch=NULL, batch2=NULL, covariates=NULL, design=matrix(1,ncol(x),1), ...) I have log cpm withTMM normalised data with covariates like sex, age and control gene expression. I don't have batch information. Could i keep batch ar ...
written 21 months ago by prathap17080 • updated 21 months ago by Gordon Smyth38k
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Comment: C: Limma RNA seq analysis_VOOM
... Thanks Gordan for your prompt reply.  I have one more doubt. In my case, is the 1st coefficient is comparison of MHO with MHNW, 2nd coefficient is comparison  of  MAO with MHNW and 3rd coefficient is comparison of MAO with MHW . Please let me know, if I understood wrong. Please find my code below. ...
written 21 months ago by prathap17080 • updated 21 months ago by Gordon Smyth38k
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Comment: C: Limma RNA seq analysis_VOOM
... Thanks a lot Smyth. As my data is now adjusted for covariates like age,sex and control gene expression. where will be this adjusted data was stored?  As per the R script mentioned below, it won't be v$E expression data. My doubt is , is it in vfit or efit? # Usual limma pipeline vfit <- lmFit(v ...
written 21 months ago by prathap17080 • updated 21 months ago by Gordon Smyth38k
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Limma voom RNA-seq analysis with both categorical and continuous confounders
... Hi, I have few doubts while using design matrix and voom function in limma 1st doubt: I'm working on RNA seq data to find out differentially expressed genes for a group where three conditions exist. I would like to include gender, age and one of the control gene expression as confounders in the des ...
limma voom written 21 months ago by prathap17080 • updated 21 months ago by Gordon Smyth38k

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