User: mforde84

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mforde84450
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Posts by mforde84

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Comment: C: "Separate enrichment analysis of pathways for up- and downregulated genes"
... We filter like this a lot for certain down stream analyses. For example, GO term enrichment analysis is a good example. Seems to me that were just talking about the differences between one and two tailed significance testing. Two tailed is going to be more conservative because the threshold pvalue i ...
written 17 days ago by mforde84450
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Comment: C: How can I find out the Linux version and what is the ftp command to install R an
... Ok, Tom, I don't mean to be a dick, but installation of R is about as well documented as it comes. If you're having trouble with the command line, then you're gonna have the same problem with R as it's a command line interface as well. And there's the inherent problem. You really cant hide that you ...
written 17 days ago by mforde84450
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Comment: C: No differentially expressed genes using DESeq2
... Maybe there's no DEG. Actually, seems like the most probably interpretation. Not unheard of. For example, shuffle your samples to generate random data, then rerun the analysis. In theory, the number of significant raw pvals should be about 5% of your total test set. ...
written 17 days ago by mforde84450
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Answer: A: Is it possible/recommended to trim RNA-Seq reads to a specific length
... fastax-trimmer - http://hannonlab.cshl.edu/fastx_toolkit/ Will get the job done. Why not give it a try? If you want to test it out, run a alignment and differential expression analysis with the regular and trimmed reads, and see how well they compare. Also the 5' of the read in RNAseq is more noise ...
written 17 days ago by mforde84450
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Answer: A: How can I merge two data frames in R with turning one of them?
... #reorder df1 so it has the same order of rows as df2 df1 <- df1[df2$Name,] #transpose df2 df2 <- t(df2) #all column names to the transposed df2 colnames(df2) <- df2[1,] #drop the first two rows in the new df2 df2 <- df2[-c(1,2),] #merge df3 <- c ...
written 18 days ago by mforde84450
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Answer: A: How can I correct skewed distribution of FPKM values?
... If the values aren't normally distributed then you'll have to use statistical test which either uses the type of distribution it is, or use a non-parametric (rank order tests etc). Since it's RNAseq data as well, my assumption is that the raw counts data follows a negative binomial distribution. So ...
written 4 weeks ago by mforde84450
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Comment: C: NGS Sequencing depths
... sorry, my bad, a misinterpretation on my end. ...
written 5 weeks ago by mforde84450
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Comment: C: Any better ways to filter GATK Mutect2 output?
... agreed. when people say stuff like the exonic mutation rate is on average 1 per kb, they are talking about germline calls. so if your looking at wgs or exome, then yea you might see 10s of thousands of events (the majority of which are probably non-synonymous and or high MAF). frequencies of somatic ...
written 5 weeks ago by mforde84450
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Comment: C: NGS Sequencing depths
... ah, i missed that. my bad. ...
written 5 weeks ago by mforde84450
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Comment: C: RNA-seq: bias in coverage
... I'm not sure you can really avoid the bias. If exon 1 on average has significantly higher CG content than exon N, then thats just the fact of the matter. ...
written 5 weeks ago by mforde84450

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