User: Papyrus

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Papyrus680
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Posts by Papyrus

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Comment: C: Understanding 'destrand' option in Bioconductor MethylKit
... I'd say the way to handle it depends on the biological question at hand. Indeed, merging strands focuses on the CpG sites and ignores hemimethylation. On the other hand, the great majority of studies on DNA methylation focus on CpG sites and do not study hemimethylation. Is the study of hemimethyla ...
written 14 days ago by Papyrus680
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Comment: C: problem changing color for annotations
... Glad to know it worked out in the end! Indeed, the names of the elements of the list (element `my_colour$condition` in this example) must match the columns of your annotation `df` (column `df$condition`). And the names of the vector of colors within each element in the list ( `CD4T_KO_NS` `CD4T_KO ...
written 16 days ago by Papyrus680
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Comment: C: problem changing color for annotations
... In that example it reads `conditions`, but it should be `condition`. Did you check that? This example works for me: counts <- matrix(1:8,4,2) colnames(counts) <- c("l1","l2") rownames(counts) <- c("a","b","c","d") my_colour <- list(condition = c(l1 = "orange", l2 = "sky ...
written 17 days ago by Papyrus680
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Comment: C: problem changing color for annotations
... It's a bit hard to see within the loop structure, and without showing your error message, but I believe your problem may be that when you create the list to define your colors: my_colour = list(df=c(l1="orange", l2="skyblue")) The internal variable should be named like the column of the annota ...
written 20 days ago by Papyrus680
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Answer: C: Understanding 'destrand' option in Bioconductor MethylKit
... I believe this refers to merging the counts of the cytosines for that CpG site. Both the C at the + strand, and the other C at the - strand (minus 1 position) belong to the same CpG site. They are not 2 different CpG sites (you could look at the site from the perspective of the "+" strand or of the ...
written 21 days ago by Papyrus680
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Comment: C: Too many Terms after Enrichment analysis
... Also, if you are specifically interested in GO terms and have too many, there are some tools which will reduce and summarize redundant lists of the terms, such as REViGO. ...
written 22 days ago by Papyrus680
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Answer: A: How to find commonly differentially expressed genes between two conditions
... intersect(dataframe1$gene_column, dataframe2$gene_column) (but not actually a bioinfo question) ...
written 23 days ago by Papyrus680
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Comment: C: Should I cluster and PCA the whole sample or only the genes of interest?
... Sorry, I just mentioned that for the sake of explaining why "information" about covariates such as batches may be in genes which are not the subset of genes of interest (for example see the [RUVSeq][1] package). But this is not directly related to your question, I did not mean to be confusing. These ...
written 25 days ago by Papyrus680
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Answer: A: Should I cluster and PCA the whole sample or only the genes of interest?
... If you want to know about batch effects, which are often methodological, or in general any covariate, I think you should investigate on all of the genes because those type of biases will be present in all of your genes (i.e. your genes of interest a priori should not be biased towards being more or ...
written 26 days ago by Papyrus680
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Comment: C: Why enrichGO does not return any enrichment terms?
... No, I meant to say the same thing that Kevin (much more clearly) stated: that you should set the same p-value, q-value thresholds (to 1, to capture all the results), to really compare, because the functions may be filtering the results differently. If, after checking that the functions are being us ...
written 29 days ago by Papyrus680

Latest awards to Papyrus

Centurion 10 weeks ago, created 100 posts.
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What to choose as background genes in GO enrichment analysis
Scholar 10 weeks ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 3 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What to choose as background genes in GO enrichment analysis
Supporter 3 months ago, voted at least 25 times.
Scholar 3 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 3 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What to choose as background genes in GO enrichment analysis
Scholar 7 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 8 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 8 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What to choose as background genes in GO enrichment analysis
Scholar 8 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What to choose as background genes in GO enrichment analysis
Scholar 9 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges
Scholar 9 months ago, created an answer that has been accepted. For A: Unable to perform for loop over list of GRanges

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