User: JMallory

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JMallory0
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Posts by JMallory

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Sanity Checking Mixed Factorial Proteomics Analysis Workflow Using Limma
... 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 ...
limma written 4 months ago by JMallory0 • updated 4 months ago by Gordon Smyth38k
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Comment: C: Interpreting Fold Change Calculation in Limma to Non-Statisticians: Sanity Check
... Thanks Aaron. This is exactly what I was looking for. ...
written 4 months ago by JMallory0
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Interpreting Fold Change Calculation in Limma to Non-Statisticians: Sanity Check
... 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. ` ...
proteomics limma written 4 months ago by JMallory0 • updated 4 months ago by LKal0
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Identification of Overrepresented Transcription Factor Binding Motifs in the Promoters of a List of DE Genes
... 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, ...
homer motif analysis written 21 months ago by JMallory0 • updated 21 months ago by Ou, Jianhong1.1k
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Comment: C: GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for
... Spot on. Thanks very much James.  ...
written 23 months ago by JMallory0
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GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
... 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 ...
goseq gene ontology written 23 months ago by JMallory0 • updated 23 months ago by James W. MacDonald51k
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Comment: C: Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
... 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 2.0 years ago by JMallory0
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Comment: C: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
... 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.   ...
written 2.0 years ago by JMallory0
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Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
... 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 ...
sva combat written 2.0 years ago by JMallory0 • updated 2.0 years ago by W. Evan Johnson800
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Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
... 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 ...
gage pathview gene ontology rna-seq written 2.0 years ago by JMallory0 • updated 2.0 years ago by Luo Weijun1.5k

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