User: Papyrus

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Papyrus370
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Posts by Papyrus

<prev • 77 results • page 1 of 8 • next >
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Comment: C: Downloading R 4.0.0
... are you working with [Windows][1], [Linux][2]...? (those are links to old releases) [1]: https://cran.r-project.org/bin/windows/base/old/ [2]: https://cran.r-project.org/bin/linux/ ...
written 8 weeks ago by Papyrus370
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Comment: C: "Normal" percent duplication for RRBS reads?
... I have worked with 75-90% duplication (FastQC), analyzing with Bismark, and have never performed de-duplication as is it not recommended with Bismark. For example, check out this [tutorial][1] by Felix Krueger and Simon R Andrews (Bismark creators) where they say up to 95% of duplication can be a " ...
written 8 weeks ago by Papyrus370
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Comment: C: Correlation for methylation(WGBS) data
... For correlation of genomic tracks with continuous data (irrespective of being intervals or not), I know of [StereoGene][2], but have not used it with methylation data in particular. I have sometimes done this: classified CpG sites into discrete levels (low-, medium- and high-methylation) and then t ...
written 8 weeks ago by Papyrus370
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Comment: C: Difference in Bismark output methylation call files and coverage files
... no worries, glad to help! ...
written 3 months ago by Papyrus370
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Answer: A: How to know which genes are favouring or inactivating a pathway in a gene set en
... I find this to be a hard and interesting question. When you perform enrichment, you check if your gene list is enriched in specific gene sets. For starters, these gene sets and their *meaning* are very varied depending on the database. They can be collections of loosely "related" genes in which the ...
written 3 months ago by Papyrus370
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Answer: A: enrichment analysis using cluster profiler
... (Even without going into the multiple testing problem and why you should adjust your p-values): Your hypergeometric test looks for an *association*, in this case, if your group of genes is more associated to a pathway (enriched) than expected by chance under the hypothesis of no association/enrich ...
written 3 months ago by Papyrus370
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Comment: C: p value for permutation test for gene-interaction data
... Although it usually will not make much difference, I would add that there is an argument for estimating the permutation p-value adding 1 to the numerator and denominator (so that `p-val = n + 1 / m + 1` where n is your number of hits higher or equal to your threshold and m is the number of permutati ...
written 3 months ago by Papyrus370
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Comment: C: Obtaining gene expression data from GEO
... I have scarce experience with expression array analysis. In the GSE you cite, they use Affymetrix, and I seem to remember the most common workflows used to normalize using the **RMA** algorithm. You may find this [tutorial][1] helpful. Aside from that, once you take care of background and distributi ...
written 3 months ago by Papyrus370
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Answer: C: Obtaining gene expression data from GEO
... In R, I'd suggest using the `GEOquery` package (see [tutorial][1]). When using this package, it will download the dataset directly into R. This will usually be in the form of an specific R class object (similar to an `ExpressionSet`), which will contain the matrix with expression data, metadata, etc ...
written 3 months ago by Papyrus370
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Answer: A: Specific gene labeling in a heatmap
... For the `pheatmap` package that behaviour is controlled by the `labels_row` or `labels_col` arguments. These labels are by default the rownames and colnames of your matrix. To only show specific names, set the rest to empty characters `""`. For example: You have this matrix, where the rows are gene ...
written 3 months ago by Papyrus370

Latest awards to Papyrus

Scholar 3 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 4 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 4 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What to choose as background genes in GO enrichment analysis
Scholar 4 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What to choose as background genes in GO enrichment analysis
Scholar 5 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 5 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges

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