Moderator: Kevin Blighe

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Kevin Blighe33k
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'Incrocio le dita e spero'

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Posts by Kevin Blighe

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Comment: C: question about TF enrichment analysis
... The Chi Square test seems a reasonable choice, given the data that you have accumulated. If you want to adjust it for length of promoter, why not build a regression model (somehow) and include the length as a covariate. With the model, you then extract the ANOVA Chi square p value from this: no ...
written 3 hours ago by Kevin Blighe33k
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Comment: C: TargetScan search for miR-10b-5p
... It seems AOK (all okay) for me. Can you confirm what you are doing to obtain the "*Prediction files*"? ...
written 3 hours ago by Kevin Blighe33k
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Comment: C: GATK 4 Mutect2 gives too much low depth variants
... Maybe these are down-sampled 'high quality' reads? The actual position read depth may be higher. I note that GATK's tools don't always report the true read-depth. ...
written 4 hours ago by Kevin Blighe33k
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Answer: A: Suggestions needed for mIRNA-human target prediction ?
... Hey, Here is the way that I did it: #1, *in silico* predicted gene targets In order to identify gene targets of micro RNAs (mirs), you can use miRNAtap (Pajak & Simpson, 2015). With this, you can choose different databases: - DIANA (Vlachos et al., 2012) - PicTar (Krek et al., 2015) - Tar ...
written 4 hours ago by Kevin Blighe33k
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Comment: C: get different heatmap from website and R
... It makes little sense to scale values that are already scaled. Can you confirm that changing `sccale` to `scale` improves the situation? ...
written 4 hours ago by Kevin Blighe33k
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Answer: A: regarding driver genes
... There is no real answer. You appear to understand the general idea of what is a driver gene. The opposite of this would be a 'passenger' gene, i.e., a gene that accumulates one or more somatic mutations due to the effects provoked by the driver gene. On this note, there is no real distinction betwe ...
written 14 hours ago by Kevin Blighe33k
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Comment: C: FPKM quantile normalization
... You asked the question here: https://support.bioconductor.org/p/116021/#116067 When you 'cross-post' to another website, please inform us so that our efforts are not in vain. ...
written 15 hours ago by Kevin Blighe33k
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Comment: C: Problem in using TCGAvisualize_meanMethylation function
... I encourage you to contact the TCGAbiolinks developers. The functions that they provide are very specific and not many have used them. ...
written 16 hours ago by Kevin Blighe33k
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Comment: C: FPKM quantile normalization
... Sorry, I was flying across the ocean. Glad that you got the solution. Where are the gene lengths being stored in your code, though? - presumably from *gencode.v19.annotation.gtf_withproteinids* ...
written 16 hours ago by Kevin Blighe33k
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Comment: C: Analyzing data from Agilent-023795 Human DNA Methylation Microarray 244k
... You can likely use the Wilcoxon Signed Rank test if you are comparing samples that are 'generally' similar/related. or those that are paired - it is a non-parametric test, which is the safest bet in these cases. Typically, in methylation, we obtain a p-value from a test and also the difference in me ...
written 16 hours ago by Kevin Blighe33k

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