User: JMallory
JMallory • 0
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Posts by JMallory
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... The present analysis is an exercise physiology study with a mixed factorial design. The design is as follows: Time (pre vs. post intervention; repeated measures) x Metformin status (on drug vs off drug; independent subjects) x dietary intervention (control diet vs MUFA enriched vs PUFA enriched; ind ...
written 25 days ago by
JMallory • 0
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24 days ago by
Gordon Smyth ♦ 37k
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... Thanks Aaron. This is exactly what I was looking for. ...
written 4 weeks ago by
JMallory • 0
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... I have seen this question posed elsewhere, but wanted to double check for some of my colleagues who want to make sure. It is the following: when defining contrasts in Limma, how is the syntax to be interpreted? I've included some code. If clarification is required, I can provide that as needed.
` ...
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... Hi,
I have a list of DE transcripts emerging from an analysis of RNA-seq data. I have mapped these transcripts back to their Ensembl ENSG IDs for submission to the `findMotifs.pl` function in the `HOMER` software suite http://homer.ucsd.edu/homer/microarray/index.html.
As described by the link, ...
written 17 months ago by
JMallory • 0
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17 months ago by
Ou, Jianhong • 1.1k
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... Spot on. Thanks very much James.
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written 20 months ago by
JMallory • 0
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... I have successfully conducted a gene ontology analysis using goseq. In presenting the findings of the analysis (i.e., the standard output generated by the `goseq` function) to a colleague, he quite reasonably asked which genes present in the vector passed to the `pwf` function were those associated ...
written 20 months ago by
JMallory • 0
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20 months ago by
James W. MacDonald ♦ 50k
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... I see. Yes, I have multiple transcripts/splice variants of a single gene mapping to a single Entrez ID in my user data. If I am understanding correctly, this is the source of the issue. The algorithm is simply selecting the first fold change value associated with a given gene ID for use in further c ...
written 20 months ago by
JMallory • 0
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... Peter, I have used WGCNA in the past, but was unaware of this function. As per its description in the documentation, it does exactly what I have been trying to get at for the past few weeks. Criminally underappreciated bit of code. Thank you.
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written 21 months ago by
JMallory • 0
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... Is there a way to use ComBat to return a data matrix adjusted by only numeric covariates? As implemented in SVA, ComBat allows for adjustment of data by numeric covariates, but only if a batch effect (i.e., a factor variable) is also provided. What if I just want to "clean" a data matrix of several ...
written 21 months ago by
JMallory • 0
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21 months ago by
W. Evan Johnson • 800
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... I have been using the following tutorial by Stephen Turner and Will Bush to look at some RNA-seq data.
http://www.gettinggeneticsdone.com/2015/12/tutorial-rna-seq-differential.html
Looking into GAGE's documentation, it looks like this tutorial is using it in a somewhat non-standard way. Specifica ...
written 21 months ago by
JMallory • 0
• updated
20 months ago by
Luo Weijun • 1.4k
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