Moderator: Nicolas Rosewick

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Posts by Nicolas Rosewick

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Comment: C: how to get correlation between the counts over each gene at the same timepoint (
... ok great. I modified my answer to archive the right answer. If the answer suits you you can accept the question. ...
written 7 days ago by Nicolas Rosewick7.2k
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Comment: C: Mapping transcripts to genome
... I used gmap in the past and it works well . ...
written 8 days ago by Nicolas Rosewick7.2k
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Comment: C: how to get correlation between the counts over each gene at the same timepoint (
... Use maybe the coefficent of variation : https://en.wikipedia.org/wiki/Coefficient_of_variation : `dat.coeff.var <- apply(dat,1,function(x){sd(x)/mean(x)})` ...
written 8 days ago by Nicolas Rosewick7.2k
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Comment: C: how to get correlation between the counts over each gene at the same timepoint (
... Ok so you want to check the correlation between replicates : then `cor(xx,method="pearson")` ...
written 8 days ago by Nicolas Rosewick7.2k
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Answer: A: how to get correlation between the counts over each gene at the same timepoint (
... Do you want to test the correlation between the different timepoints or between the different genes. Let say you have 10 timepoints and 58000 genes To test the different timepoints : cor(xx, method="pearson") will give you a 10x10 matrix , so 100 correlations calculation (even though I guess ...
written 8 days ago by Nicolas Rosewick7.2k
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Comment: C: Is it fine to run SVM on RNA-seq read counts?
... > If code required, let me know. Yes code **and** minimal dataset is required to help you ;) ...
written 8 days ago by Nicolas Rosewick7.2k
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Comment: C: Correlation plot by correlation values in R
... Simply reduce the width size of your plot. And your score seems not so widely distributed (between -1 and 1) as the plot you showed in your post (more between -0.1 and 0.1) ...
written 8 days ago by Nicolas Rosewick7.2k
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Answer: A: Correlation plot by correlation values in R
... use geom_jitter from ggplot library(ggplot2) library(cowplot) dat <- data.frame( sample=1:10, score=c( rnorm(n=40,mean = 0.7,sd=0.1), rnorm(n=40,mean=0,sd=0.1), rnorm(n=20,mean=-0.5,sd=0.1)), diagnoses=c( rep("ADC",40), ...
written 8 days ago by Nicolas Rosewick7.2k
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Comment: C: Brief Reminder On How To Ask A Good Question
... For R related question, usage of `dput` for minial example should be mandatory ! ...
written 11 days ago by Nicolas Rosewick7.2k
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Answer: A: Transcriptome analysis for differential gene expression
... You should : - Not do further cleaning of the fastq files - Not merge paired-end fastq files - Use STAR for alignment (BWA and bowtie2 are maint for DNA not RNA) - For the genome you can use the ENSEMBL version : https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index ...
written 12 days ago by Nicolas Rosewick7.2k

Latest awards to Nicolas Rosewick

Great Question 5 days ago, created a question with more than 5,000 views. For featureCounts exon counting problem
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 7 days ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
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Good Answer 8 days ago, created an answer that was upvoted at least 5 times. For A: How Do I Make A Heatmap In R?
Scholar 8 days ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Appreciated 8 days ago, created a post with more than 5 votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Popular Question 11 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 12 days ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Popular Question 18 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
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Scholar 3 months ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
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