User: microbiotaiota

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Posts by microbiotaiota

<prev • 26 results • page 2 of 3 • next >
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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 6 weeks 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 7 weeks 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 7 weeks 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 8 weeks ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... This works as well! Thank you. I had to change `mydata` to `myfiles`. mydata <- imap(myfiles, function(x, y) { ...
written 10 weeks ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... Thanks, I'll give it a crack ...
written 11 weeks ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... Thank you! I have given it a try, however I have run into 2 issues. Firstly, when running the below I get `duplicate 'row.names' are not allowed` and I think the this comes down to `row.names=1`. I checked the files to see if there were any duplicate Gene IDs and there weren't (`cat file.tab | cut ...
written 11 weeks ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... I have both, I thought that having each file in the same directory might make it easier. I'll be sure to clarify in future posts. ...
written 11 weeks ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... Thank you, fixed it up now ...
written 11 weeks ago by microbiotaiota20

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