User: microbiotaiota

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Posts by microbiotaiota

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Comment: C: Normalisation of paired samples in edgeR
... Great, thank you. Just saw this. I'll give this a go. ...
written 8 days ago by microbiotaiota20
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Comment: C: Normalisation of paired samples in edgeR
... Also, was it correct for me to to the PCA on the normalised data? ...
written 8 days ago by microbiotaiota20
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Comment: C: Normalisation of paired samples in edgeR
... Awesome, that'll be of great help, where will the tutorial be available? ...
written 8 days ago by microbiotaiota20
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Comment: C: Normalisation of paired samples in edgeR
... I did PCA using `plotMDS` on the raw data and on the normalised data. I have 'Leading logFC dim2' along the y-axis and 'Leading logFC dim1' along the x-axis. For the raw data the samples cluster along y=0, and after normalisation the samples are more dispersed. I'm working with circRNAs and I used ...
written 8 days ago by microbiotaiota20
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Comment: C: Normalisation of paired samples in edgeR
... Great thank you, I'll include normalisation. Yes I do start with raw counts. I have a filtering section: keep <- rowSums(cpm(y)>0.5) >=2 My groups looks like this: files group lib.size norm.factors subjects a_1 1.csv control 16065685 ...
written 9 days ago by microbiotaiota20
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Normalisation of paired samples in edgeR
... I am performing differential expression of 10 paired samples (cancer and normal tissue) in edgeR and I'm following '3.4.1 Paired samples' in the Bioconductor User's Guide. Do the library sizes need to be normalised prior to testing for treatment efftect? Normalised with: y <- calcNormFact ...
rna-seq edger written 9 days ago by microbiotaiota20
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Read counts from DCC or CIRI2 for differential expression with DESeq2?
... I am starting differential expression of circRNAs. I have used DCC and CIRI2 and have selected circRNAs detected by both methods. Do I use read counts from DCC or CIRI2 for differential expression in DESeq2? I don't think the average of read counts from DCC or CIRI2 is correct as they are differen ...
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Comment: C: Exclude non-coding genes
... Hello, I'm not familiar with Windows. There is the option to install WSL (Windows Subsystem for Linux) which lets you run the above commands on your Windows machine. Perhaps someone else can suggest a better alternative. ...
written 19 days ago by microbiotaiota20
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Comment: C: Exclude non-coding genes
... You can do this through Terminal if you are on a Mac/Linux as grep is used for Unix operating systems. 1. First `cd` to the folder/directory your files (the protein coding genes and your list containing the 6000 genes) are in: `cd /Users/your/directory/` 2. Run the `grep` command to filter y ...
written 21 days ago by microbiotaiota20
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When would you add your own library size in edgeR?
... In edgeR there is an option to add your own library size for each sample instead of letting edgeR sum the total reads for each sample. You could set your library size to total reads, uniquely mapped reads etc. In what scenarios would you want to add your own library size than to let edgeR sum the r ...
edger rna-seq written 25 days ago by microbiotaiota20

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