User: newbio17

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newbio1710
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Posts by newbio17

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Using linear regression to accounting for confounding variables in gene expressi
... 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 newbio1710
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Using linear regression to accounting for confounding variables in gene expression data
... 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 ...
linear regression rna-seq written 7 months ago by newbio1710 • updated 7 months ago by Charles Warden7.2k
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Comment: C: Correlation analysis between gene expression & tumor purity
... Thank you. Your posts are always helpful. ...
written 7 months ago by newbio1710
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Correlation analysis between gene expression & tumor purity
... 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 ...
correlation gene expression tumor purity rna-seq written 7 months ago by newbio1710 • updated 7 months ago by Devon Ryan91k
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Adding RNA-Seq reads from one sequencing experiment to reads from another experiment
... 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 ...
rna-seq written 9 months ago by newbio1710
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Detecting antisense RNA in unstranded RNA-Seq data
... 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 ...
rna antisense rna-seq written 9 months ago by newbio1710 • updated 9 months ago by caggtaagtat700
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Differential expression analysis using GFOLD and DESeq2
... 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 ...
deseq2 rna-seq gfold written 10 months ago by newbio1710 • updated 10 months ago by Kevin Blighe46k
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Comment: C: Orientation of reads in .fastq files from RNA-Seq
... 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 newbio1710
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Orientation of reads in .fastq files from RNA-Seq
... 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 ...
salmon rna-seq written 10 months ago by newbio1710 • updated 10 months ago by swbarnes26.2k
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Answer: A: Visualizing overdispersion for raw RNA-Seq data
... 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 newbio1710

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