User: shawn.w.foley

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shawn.w.foley750
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Posts by shawn.w.foley

<prev • 99 results • page 1 of 10 • next >
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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.foley750
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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.foley750
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Comment: C: Wrong results in differential gene expression analysis
... 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.foley750
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Answer: A: SNPs from RNA-Seq Compare with SNPs from DNA-Seq
... 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.foley750
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Comment: C: Converting FPKM values to raw read counts
... 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.foley750
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Comment: C: How can I solve this error when I analysis the micro-array data?
... 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.foley750
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Comment: C: Converting FPKM values to raw read counts
... 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.foley750
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Answer: A: DESeq2 results versus by eye comparison in IGV
... 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.foley750
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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.foley750
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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.foley750

Latest awards to shawn.w.foley

Scholar 12 days ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Scholar 12 days ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Commentator 19 days ago, created a comment with at least 3 up-votes. For C: Middle author, but not first author projects. How would you approach this?
Scholar 4 weeks ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Popular Question 5 weeks ago, created a question with more than 1,000 views. For ChIP-seq differential binding with multiple replicates using MACS2 bdgdiff.
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Scholar 7 weeks ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Scholar 9 weeks ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Middle author, but not first author projects. How would you approach this?
Scholar 3 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Supporter 3 months ago, voted at least 25 times.
Student 3 months ago, asked a question with at least 3 up-votes. For Analyzing RNA-seq without replicates
Popular Question 7 months ago, created a question with more than 1,000 views. For Analyzing RNA-seq without replicates
Scholar 7 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Popular Question 9 months ago, created a question with more than 1,000 views. For Analyzing RNA-seq without replicates
Scholar 17 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Scholar 18 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c

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