Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis23k
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Location:
National Institutes of Health, Bethesda, MD
Website:
http://watson.nci.nih....
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seandavis12
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Posts by Sean Davis

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Comment: C: Convert chromosome headings in VCF file from Trinity format to chr:pos format
... Do you know how to convert from your custom transcript locations to genome locations? What organism are you working with? ...
written 23 days ago by Sean Davis23k
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Answer: A: Question on number of probes in CEL and SOFT from GEO
... The original submitters apparently filtered the data. That is not uncommon. ...
written 23 days ago by Sean Davis23k
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Comment: C: Calculation of number of raw reads, Q30, GC content for raw data QC
... These numbers are functionally the same. No, I would not merge the fastq files. I would report two Q30 numbers and two GC numbers. In all cases where the experiment "worked" as expected, the numbers for read 1 and read 2 will be quite similar. If they are not, you NEED to know that. ...
written 9 weeks ago by Sean Davis23k
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Comment: C: Calculation of number of raw reads, Q30, GC content for raw data QC
... I'd report both forward and reverse Q30 and GC from FastQC, so four numbers. This is for quality control, so having all values available will avoid "hiding" bad data. ...
written 9 weeks ago by Sean Davis23k
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Answer: A: How to perform GSEA analysis with survival phenotype?
... Your approach of using cox regression to get an ordered list of genes is fine. From there, you can proceed to threshold based on some cutoff for significance or use a rank-based GSEA approach. ...
written 9 weeks ago by Sean Davis23k
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Answer: A: Add GenomicRanges to SummarizedExperiment
... Using resGR <- results(RAW_DESeq2AF, lfcThreshold = 1, format = "GRangesList") or resGR <- results(RAW_DESeq2AF, lfcThreshold = 1, format = "DataFrame") should address the issue. ...
written 9 weeks ago by Sean Davis23k
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Answer: A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
... Take a look at ggbio. https://bioconductor.org/packages/ggbio https://www.google.com/search?q=ggbio&tbm=isch ...
written 9 weeks ago by Sean Davis23k
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Answer: A: Install DESeq2 and edgeR with Anaconda
... The Bioconductor project does not support bioconda directly, so your mileage may vary when using bioconda. The recommended way to install Bioconductor packages is from within R using: source("https://bioconductor.org/biocLite.R") biocLite("DESeq2") biocLite("edgeR") ...
written 9 weeks ago by Sean Davis23k
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Comment: C: how to extract highly correlated genes in interaction network ?
... It sounds like you'll need to learn some R before proceeding. Being able to select subsets of data in R is a skill that will serve you well. You can still use WGCNA after subsetting your data if it suits your needs. ...
written 9 weeks ago by Sean Davis23k
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Answer: A: how to extract highly correlated genes in interaction network ?
... You may not need the WGCNA package at all if you simply want to get correlations. Take a look at the `cor` function in R. That said, no matter what you end up doing, you will definitely want to filter your genes before doing the correlation. Only about 50% of the genes are likely expressed in eac ...
written 10 weeks ago by Sean Davis23k

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