User: Nithisha

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Nithisha10
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11 months, 4 weeks ago
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Posts by Nithisha

<prev • 42 results • page 2 of 5 • next >
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Comment: C: Standardizing gene symbols
... Thanks a lot Gordon.  I do have a few questions though. For your code, I did not completely understand what  fit$genes$Official.Symbol refers to. Is that pointing to a dataframe within another dataframe? I used this: dfl$Official_Symbol <- alias2SymbolTable(df$gene, species="Mm") where df i ...
written 10 months ago by Nithisha10
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Solve overlapping gene labels in volcano plot when using textxy
... Hi everyone,  This is the code I used to create a volcano plot: I am trying to plot several genes and highlight the top 20 most downregulated and top 20 most downregulated genes using green and red. #Plot a volcano plot library(calibrate) head(afinal) threshold.high <- afinal$logFC[20] ...
R written 11 months ago by Nithisha10
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Comment: C: Standardizing gene symbols
... Hi Simon, Some lists are from mice and some are from humans. Would this cause problems? ...
written 11 months ago by Nithisha10
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Standardizing gene symbols
... Hello all, I have a list of gene symbols that I obtained after querying CHEMBL and a separate list of gene symbols from querying datasets from GEO and using Limma on them. When I try to compare both lists, I find that I cannot look for similar gene symbols as gene synonyms exist. An example would ...
R written 11 months ago by Nithisha10 • updated 11 months ago by Gordon Smyth35k
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Comment: C: Volcano Plot (highlighting top genes in a different color)
... Thank you, I shall try this out! ...
written 11 months ago by Nithisha10
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Volcano Plot (highlighting top genes in a different color)
... Hi everyone, I am trying to plot Volcano plots for analysis mostly from Limma. I found 2 sources- one that labels points above certain thresholds of adjusted p values and logFC values and another one that uses the MarrayLM object as input and labels the top gene hits. Here are the source links: 1 ...
volcanoplot written 11 months ago by Nithisha10 • updated 11 months ago by thokall120
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Comment: C: DEG with Limma without replicates and best plots to represent results
... Hi Aaron, Thank you, that makes a lot of sense! ...
written 11 months ago by Nithisha10
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Comment: C: Using R for EnrichR analysis
... Thank you Gordon, I shall try that! ...
written 11 months ago by Nithisha10
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Comment: C: DEG with Limma without replicates and best plots to represent results
... Hi Aaron, Thank you so much, this explains a lot, appreciate the help. Just to clarify, when we make a contrast matrix and in the final output for fit2$coefficients, we get +2 for groupsA-groupsB for Gene A, this would mean that Gene A was down regulated by (lg2) times in groupsB with respect to g ...
written 11 months ago by Nithisha10
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DEG with Limma without replicates and best plots to represent results
... Hi all, I have a few questions regarding Limma. 1) I am asking a question with reference to https://support.bioconductor.org/p/48601/#102609. This is a case where there are no replicates for samples, and we cannot run eBayes or toptable. I understand that running fit2$coefficients will bring out l ...
limma written 11 months ago by Nithisha10 • updated 11 months ago by Aaron Lun21k

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Supporter 11 months ago, voted at least 25 times.

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