User: User34591

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User345910
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Posts by User34591

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Comment: C: Plotting for mutational burden - R package
... Hi, sorry to re-open this post did you find a way to do the plot at the top ? I am very very interested !! Thank you ! ...
written 12 months ago by User345910
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Comment: C: Combine RNAseq datasets vst + Combat
... I see your point, thank you ! I know this is really tricky. I will try what you have suggested. Again thank you for your help ! ...
written 3.1 years ago by User345910
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Comment: C: Combine RNAseq datasets vst + Combat
... I am not sure to understand how  GC correction will correct for protocol and batch effect ? ...
written 3.1 years ago by User345910
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Comment: A: Combine RNAseq datasets vst + Combat
... Many thanks for your reply. My goal is to describe my dataset according to TCGA data. Does my samples have same expression level than those from TCGA for a set of genes (boxplot and PCA/clustering if possible). The absolute expression level is not really important I am more interested by the trend. ...
written 3.1 years ago by User345910
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Combine RNAseq datasets vst + Combat
... Hi, I have a home made RNAseq dataset, and I would like to compare the expression of some genes to TCGA samples (public data). I am not talking about differential analysis here, rather descriptive analysis. What I would like to do is to first "vst transforme" all data together, then apply Combat on ...
deseq2 combat vst written 3.1 years ago by User345910
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Clustering with differentially expressed genes in RNAseq
... I have performed differential analysis with DESeq2, edgeR and voom-limma. My goal was to evaluate each methods on my data. Now I would like to perform clustering with the genes found differentially expressed (DEG) by each method to see how well these genes discriminat my two conditions. To do so, I ...
edger deseq2 limma voom written 3.6 years ago by User345910 • updated 3.6 years ago by Aaron Lun25k
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cellHTS2 : negative values after normalization
... Hello everyone, I am new in HTS data and there is a point that I don't really understand. I want to analyse data from viability assays , for which I have positive and negative controls. So, I am interested in the quantity x_i / mean(x_controlPos) in order to select wells with less living cells tha ...
cellhts2 written 4.2 years ago by User345910 • updated 4.2 years ago by Joseph Barry160

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Clustering with differentially expressed genes in RNAseq

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