User: mrodrigues.fernanda

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10
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New User
Location:
University of Illinois, Urbana-Champaign
Last seen:
6 months, 3 weeks ago
Joined:
1 year, 10 months ago
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f*******@illinois.edu

Posts by mrodrigues.fernanda

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Using SVA with RRBS data
... Jeff, Thank you for your response. I read of people using sva, but I am not sure on how to put the data in the right format for it. The reason why I want to use sva in this data is that I am almost certain of the existence of unknown batch effects. I have used the same samples for RNA-seq data, whe ...
written 8 months ago by mrodrigues.fernanda10
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Using SVA with RRBS data
... Hello I have seen a lot of posts with this question, but have not found an answer to this. I am analyzing my RRBS data with methylKit, and I can see in my PCA plots that there are some batch effects. Is there a way to use SVA to estimate surrogate variables from methylation data? If yes, how to do ...
sva rrbs written 8 months ago by mrodrigues.fernanda10 • updated 8 months ago by Jeff Leek490
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Comment: C: ExportingWGCNA data for Ingenutity IPA
... Thank you for your response, Peter! I think you answered my question.  I was using cytoscape to visualize the network WGCNA created, so I guess I will just stick to that.   ...
written 9 months ago by mrodrigues.fernanda10
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ExportingWGCNA data for Ingenutity IPA
... Hi I have RNASeq data for which I performed differential expression analysis (using the R package edgeR) and gene coexpression analysis using the R package WGCNA in order to separate my genes into gene modules. I see that wgcna has functions to export its data to cytoscape and visant for network vi ...
wgcna ipa network visualization written 9 months ago by mrodrigues.fernanda10 • updated 9 months ago by Peter Langfelder1.3k
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Comment: C: goseq: not able to limit by GO categories when using wallenius approximation for
... Thank you for the clarification!! ...
written 19 months ago by mrodrigues.fernanda10
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Comment: C: goseq pwf length bias plot: help interpreting plot
... Hi Nadia! I tried including all genes in the analysis (without any previous filtering) and now I get a regular plot, like in the tutorial. It seems like the problem has been solved. Thank you so much for your help! ...
written 19 months ago by mrodrigues.fernanda10
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goseq: not able to limit by GO categories when using wallenius approximation for over-representation test
... Hi Guys Here I am again with another question about goseq. I am following the goseq tutorial. I am manually inserting my length and go data, since the combination o fmy species genome and gene ID is not supported by goseq.  I ran the following code, and it ran fine as you can see in my output: G ...
goseq written 19 months ago by mrodrigues.fernanda10 • updated 19 months ago by Nadia Davidson260
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Comment: C: goseq pwf length bias plot: help interpreting plot
... Hi Nadia Thank you so much for your response and e-mail. Regarding my analysis previously to go seq, I analyzed my RNA-seq data for differential expression using sva (due to the presence of unknown batch effects) and edgeR. I obtained 507 differentially expressed genes at a 0.01 FDR. And all genes ...
written 19 months ago by mrodrigues.fernanda10
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Answer: A: Plot with two separated groups of genes.
... Not sure of what your data looks like, and how you're analyzing it, but the plotPCA() function from the affycoretools R package may allow you to do that. You can also produce a 3d plot with this function. ...
written 19 months ago by mrodrigues.fernanda10
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Comment: C: Weird result with GOseq
... Hi! I know this is a bit late, but have you ever figured out why your plot looked like that? I obtained similar results with my data. Except I'm working with bovine. ...
written 19 months ago by mrodrigues.fernanda10

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Popular Question 6 months ago, created a question with more than 1,000 views. For sva + egdeR - differential expression analysis - RNA-seq data

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