User: nooshin

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nooshin290
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Posts by nooshin

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GOSemSim - slow for BP terms
... Hi, I'm using GOSemSim to find similarity between genes based on their annotation with respect to BP, CC, and MF. I realized that the speed of the algorithm for BP terms are very much slow. If I ran my algorithm even in parallel with these 3 terms, CC and MF is going to finish, and the BP starts ...
gosemsim go enrichment go semantic similarity written 5 months ago by nooshin290
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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 2.8 years ago by nooshin290
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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 2.8 years ago by nooshin290
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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 2.8 years ago by nooshin290
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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 2.8 years ago by nooshin290 • updated 2.8 years ago by Gordon Smyth37k
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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 2.8 years ago by nooshin290
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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 2.9 years ago by nooshin290
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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 2.9 years ago by nooshin290
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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 2.9 years ago by nooshin290 • updated 2.9 years ago by Michael Love23k
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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 3.0 years ago by nooshin290

Latest awards to nooshin

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Error in .checkKeys(value, Lkeys(x), x@ifnotfound)
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Motif search
Popular Question 2.7 years ago, created a question with more than 1,000 views. For error ReadAffy

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