User: nooshin

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nooshin270
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Posts by nooshin

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Comment: C: RNA-seq: two factor anova - how to find the variability explained by each of the
... Then this means that I can do the same anova analysis on logCPM values for each gene. Thanks a lot. ...
written 15 months ago by nooshin270
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Comment: C: RNA-seq: two factor anova - how to find the variability explained by each of the
... would you mind please guide me on how I can do it? tnx   ...
written 15 months ago by nooshin270
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Comment: C: RNA-seq: two factor anova - how to find the variability explained by each of the
... v2 is a less biased indicator of variance explained in the population by a predictor variable: (SS_factor - df*(MS_residual))/ (SS_total + MS_residual) It's basically the same as V1 but the normalized version if it's possible to call it so :) ...
written 15 months ago by nooshin270
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Comment: C: RNA-seq: two factor anova - how to find the variability explained by each of the
... Thanks a lot for your response. Yes, I want the SS and MS for each gene separately like in anova. I need to calculate the variabilities of each factor and their interactions separately for each gene, like the following example by using anova: res <- anova(lm(values ~ Sex*Time,data)) res_s ...
written 15 months ago by nooshin270 • updated 15 months ago by Gordon Smyth32k
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RNA-seq: two factor anova - how to find the variability explained by each of the factor?
... Hi all, I have to do two way anova on the RNA-seq data and find out the variability that can be explained by each factor: Time <- factor(rep(1:3,4),levels=3:1) Sex <- factor(rep(c("Female","Male"),each=6),levels=c("Male","Female")) design <- model.matrix(~Sex*Time) I want to calcula ...
rnaseq limma edger deseq2 two factor anova written 15 months ago by nooshin270
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Comment: C: Error in (function (classes, fdef, mtable) : unable to find an inherited met
... Thanks a lot for your help. I will follow the instruction and make a new post in case of facing an error.   ...
written 17 months ago by nooshin270
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Comment: C: Error in (function (classes, fdef, mtable) : unable to find an inherited met
... thanks a lot for your response, but it says that edgeR does not exist for R 3.3 :( ...
written 17 months ago by nooshin270
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Error in (function (classes, fdef, mtable) : unable to find an inherited method for function assayNames for signature "DESeqDataSet"
... Hi, I want to use DESeq2 to find deferentially expressed genes under specific condition, however it produces strange error: > dds <- DESeqDataSetFromMatrix(countData = counts,colData = colData,design = ~ condition + time) Error in (function (classes, fdef, mtable) : unable to find an inh ...
deseq2 error written 17 months ago by nooshin270 • updated 17 months ago by Michael Love14k
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Comment: C: edgeR - making 12 contrast but only get 5 contrasts as a result
... Thanks a lot. It was my mistake to use edgeR similar as limma. Now all is clear, tnx ...
written 17 months ago by nooshin270
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Comment: C: edgeR - making 12 contrast but only get 5 contrasts as a result
... Just as a very short question, is this concept in edgeR then different from limma? Since in limma, I get all specific contrasts separately when I run: c.fit=contrasts.fit(fit,mc)   ...
written 17 months ago by nooshin270

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