User: DataFanatic

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DataFanatic200
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Posts by DataFanatic

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Comment: C: Differential gene expression analysis
... Sure. This doesn't answer my question. ...
written 2 days ago by DataFanatic200
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Comment: C: Differential gene expression analysis
... Unfortunately, I cannot add more details. This information should be enough to answer my original question: Does DESeq2 expect a minimum number of genes? ...
written 2 days ago by DataFanatic200
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Comment: C: Differential gene expression analysis
... Of course, I know I can filter, people filter for example low expressing genes, etc. I was hoping for guidance and insights on the statistical assumptions to better understand how I can partition my data. ...
written 2 days ago by DataFanatic200
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Differential gene expression analysis
... I am performing differential gene expression using DESeq2 but will be subsetting transcripts based on a pre-determined criterion. Does this sub-setting violate any assumptions make by the statistical package? ...
deseq2 rna-seq written 2 days ago by DataFanatic200 • updated 2 days ago by swbarnes27.8k
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Comment: C: How to estimate the inter sample and inter replicate correlation coefficient?
... The cor function does what I was expecting to do. For example form a counts matrix a=cor(counts(dds)) cor.samples=corrplot(a, method="number") Will produce a plot such as this one: https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html But I would like to show a li ...
written 22 days ago by DataFanatic200
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Comment: C: How to estimate the inter sample and inter replicate correlation coefficient?
... Okay thanks. How is this done in R? and how can I actually print the r2 value? I know how to do and plot PCA but not sure how I can get the r2 value.. Also, is there a way to perform this analysis on the fastq files before alignment? ...
written 22 days ago by DataFanatic200
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How to estimate the inter sample and inter replicate correlation coefficient?
... How to estimate the inter sample and inter replicate correlation coefficient? My dataset consists of 2 RNA-Seq samples treatment and control and each sample has 3 replicates. I would like to show that the replicates have a higher correlation coefficient than that of the samples( treatment and contro ...
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Comment: C: Can someone explain in detail the meaning of a gseaplot in GSEA
... Thanks genomax, this was very helpful! ...
written 24 days ago by DataFanatic200
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Comment: C: Can someone explain in detail the meaning of a gseaplot in GSEA
... For example, are the most statistically significant genes on the left or right?; or, are those with largest fold-change on the left or right? This is an example I found online. In my case, I'm using the log2foldchange and ranked in decreasing order so high to low. I understand from your answer, the ...
written 24 days ago by DataFanatic200
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Can someone explain in detail the meaning of a gseaplot in GSEA
... Can someone explain in detail the meaning of a gseaplot in GSEA https://yulab-smu.github.io/clusterProfiler-book/clusterProfiler_files/figure-html/gseaplot-1.png ...
gseaplot written 25 days ago by DataFanatic200 • updated 24 days ago by Kevin Blighe60k

Latest awards to DataFanatic

Popular Question 14 days ago, created a question with more than 1,000 views. For Filter out related individuals from a vcf file using Plink or Hail
Popular Question 26 days ago, created a question with more than 1,000 views. For Filter out related individuals from a vcf file using Plink or Hail
Centurion 5 weeks ago, created 100 posts.
Popular Question 12 months ago, created a question with more than 1,000 views. For Filter out related individuals from a vcf file using Plink or Hail
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Great Question 18 months ago, created a question with more than 5,000 views. For merging two bigwig files
Popular Question 18 months ago, created a question with more than 1,000 views. For Filter out related individuals from a vcf file using Plink or Hail
Popular Question 18 months ago, created a question with more than 1,000 views. For merging two bigwig files
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
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Popular Question 3.1 years ago, created a question with more than 1,000 views. For merging two bigwig files

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