User: shawn.w.foley
shawn.w.foley • 750
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Posts by shawn.w.foley
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Comment:
C: Somatic mutations per gene
... As far as counting, I don't know of any, but `snpEff` can annotate SNPs, mapping them to genes and qualifying them as "HIGH", "MEDIUM", or "LOW" severity. You can then filter for SNPs that are meaningful to your project.
From there you could load the data into R, convert the gene data into a `fact ...
written 4 days ago by
shawn.w.foley • 750
2
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49
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Answer:
A: MACS2 result of FDR
... An FDR (or q-value) is an adjusted p-value, therefore the lowest q-value is the most significant. However, in this case you're not looking at q-values, but at -log10(q-value), in which case the highest number is more informative (because of that negative sign). For example, if q = 10^-10 that's a hi ...
written 4 days ago by
shawn.w.foley • 750
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... As h.mon said, without more information it's impossible to know what's causing these differences.
To hazard a guess, did you flip comparison? The paper shows 12 upregulated and 4 downregulated genes. If you're seeing 27 downregulated and 3 upregulated genes you could have the denominator and numera ...
written 6 days ago by
shawn.w.foley • 750
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... One of the major challenges to this analysis is that different SNP finding algorithms will yield drastically different results. I'd recommend using the GATK best practices for your DNA-seq (they have different protocols for WGS and WES), and for your RNA-seq. Using their pipelines to call SNPs will ...
written 6 days ago by
shawn.w.foley • 750
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128
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... I'd be a little concerned about mixing RNA-seq and microarray expression data - yes they'll both be on a log scale but they'll still be on quite different scales (microarray signal intensity is generally on a 6-12 range, while the log2(FPKM) would be ~1-13). I'd put a little more thought into combin ...
written 10 days ago by
shawn.w.foley • 750
1
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... What code are you running that leads to this error? What's the input data look like? Is this raw CEL files or some partially processed data? We need more detailed information to advise. ...
written 10 days ago by
shawn.w.foley • 750
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... What you're describing isn't converting the FPKM values to raw reads, but filtering genes based on FPKM levels. If that's the end goal then I see no harm in your analysis. I do have a couple of questions:
Why are you filtering for expression in 10 samples? Would it be more appropriate to require ex ...
written 10 days ago by
shawn.w.foley • 750
2
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119
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... As swbarnes2 said, the biggest question is going to be normalization. What **exactly** is in IGV? Are you just looking at counts? Have you normalized for sequencing depth? I see both tracks are on the same scale, but does that blue track actually go above 90? I'd also say that DESeq2 is reporting a ...
written 11 days ago by
shawn.w.foley • 750
0
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144
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Comment:
C: issue with ifelse statement
... Apologies for the Typo, I misread column names in the OP, I've edited my answer. ...
written 11 days ago by
shawn.w.foley • 750
4
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2
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144
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2
answers
Answer:
A: issue with ifelse statement
... It looks like the `ifelse` command isn't meant to be nested like you have in your code, it's for binary output and it seem like you want three options (`1`, `2`, or `NA`). From the man page:
Usage:
ifelse(test, yes, no)
Arguments:
test: an object which can be coerced to log ...
written 12 days ago by
shawn.w.foley • 750
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