User: newbio17
newbio17 • 10
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Posts by newbio17
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... To clarify, I'm attempting to replicate the correlation analysis that was done in the paper below: https://www.biorxiv.org/content/biorxiv/early/2018/09/20/422592.full.pdf
One of the steps that they perform is adjusting the expression levels of all samples according to tumor purity using linear reg ...
written 7 months ago by
newbio17 • 10
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... My data consists of 20,000 rows (genes) and 300 columns (samples). 5 out of 300 are cell lines and 295 out of 300 are tumor samples.
I'm currently attempting to adjust the expression values according to a confounding variable using linear regression. In summary, I have a dataframe consisting of the ...
written 7 months ago by
newbio17 • 10
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7 months ago by
Charles Warden ♦ 7.2k
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... Thank you. Your posts are always helpful. ...
written 7 months ago by
newbio17 • 10
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... What I have seen previously in papers is that the authors find genes that are highly correlated with tumor purity.
- [Paper #1][1]
- [Paper #2][2]
I'm mainly confused in Paper #1, when author says:
> "Spearman correlations were calculated between their expression and tumor purity to generate ...
written 7 months ago by
newbio17 • 10
• updated
7 months ago by
Devon Ryan ♦ 91k
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... We outsourced some RNA-Seq experiments to a 3rd-party vendor. When we first received our data, they notified us that the number of reads generated did not match the number of reads guaranteed in the quote. So they told us that they will do additional sequencing if we agreed to wait 5-10 days. The fi ...
written 9 months ago by
newbio17 • 10
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... I've gone over a couple of previous questions discussing a similar subject and they seem to all imply that it simply is not feasible to do with unstranded RNA-Seq data.
We know that for RNA-Seq, RNA is reverse transcribed into cDNA and that antisense RNA is complementary to its mRNA on the sense st ...
written 9 months ago by
newbio17 • 10
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9 months ago by
caggtaagtat • 700
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... Details about the experiment can be found on bioconductor page below:
[Bioconductor post][1]
The author of DESeq2 mentioned that I cannot get analysis results for interaction between type and time due to the number of samples.
Since GFOLD is specifically designed for doing analysis without replic ...
written 10 months ago by
newbio17 • 10
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10 months ago by
Kevin Blighe ♦ 46k
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... Thank you genomax. However, table seems a little bit confusing to me.
From what I'm able to understand, if library kit *Illumina TruSeq Stranded Total RNA* was used, then reads from reverse-strand belongs to 1st read strand? If this is correct, this is why I would have to use ISR instead of ISF? ...
written 10 months ago by
newbio17 • 10
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... I have R1.fastq and R2.fastq from RNA-Seq experiment. I'm currently trying to perform differential expression using Salmon and DESeq2.
Since the RNA-Seq was done using stranded library kit, it was under my assumption that R1.fastq contains forward reads and R2.fastq contains reverse reads.
So, I u ...
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... Answered by Devon. Thanks!
> Most differential expression packages (DESeq2 and edgeR) include the steps for making such plots in their tutorials. ...
written 11 months ago by
newbio17 • 10
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