User: detroit.drive

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Posts by detroit.drive

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biotmle package error with heatmap/dendrogram
... Hello, I'm following the biomarker pipeline found in the biotmle package and ran across an error with the heatmap/dendrogram command (see below). heatmap_ic(x = limmaTMLEout, +            row.dendrogram = TRUE, +            clustering.method = "hierarchical", +            design = design, FDRcutoff ...
biotmle written 7 hours ago by detroit.drive0
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(Closed) Gene Expression won't work because arguments imply differing number of rows
... I'm using the ALL dataset from Bioconductor. My task is to convert the “BT” attribute to categorical variables with just two levels, “B” and “T” and then test all genes for significant association with B/T disease subtype using ANOVA and then plot the p-values. As a solution I performed the followi ...
R all written 3 months ago by detroit.drive0 • updated 3 months ago by James W. MacDonald48k
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Comment: C: Building linear model (age effect on gene expression)
... Many thanks Gordon!  Let me try to break down what you've accomplished for my own understanding.  First, for the !is.na(age) snippet - this is what's telling the code to create a variable (ALL2) which represents the entire (12625) matrix?  Next, for the design step, you did the opposite of what I di ...
written 4 months ago by detroit.drive0
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Building linear model (age effect on gene expression)
... For the past few weeks I've been posting about devising a way to build linear models and plot them using the ALL dataset.  Specifically a linear model for the effects of age on gene expression.  Up to this point I've only been able to develop a model for 1 individual gene (probe id) but because my R ...
linear model bioconductor all written 4 months ago by detroit.drive0 • updated 4 months ago by Gordon Smyth35k
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Comment: C: ALL dataset, correct syntax using the exprs call?
... Martin, I found this webpage you put together a few years ago (https://www.bioconductor.org/help/course-materials/2016/BiocIntro-May/A3_Statistical_Analysis.html).  I'm wondering if its possible to adapt your code so it builds a linear model for age effect on gene expression in ALL.  You have the fo ...
written 4 months ago by detroit.drive0
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Answer: A: Tutor Wanted: help with R statistical analysis (must be familiar with Bioconduct
... Hi Gordon - do you think you could serve as a tutor? ...
written 4 months ago by detroit.drive0
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Comment: C: ALL dataset, correct syntax using the exprs call?
... Hi Martin and other Bioconductors, I've updated my packages to include limma and developed the following model: > ourData <- exprs(ALL) > ourDataFactor <- ourDataFactor <- pData(ALL)$age > design <-model.matrix(~ ourDataFactor) > fit <- lmFit(ourData, design) > fit ...
written 4 months ago by detroit.drive0
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Job: Tutor Wanted: help with R statistical analysis (must be familiar with Bioconductor)
... Hello, I was seeking a tutor that could help me with a R course - this is no longer needed, thanks everyone! ...
job R bioconductor all written 4 months ago by detroit.drive0
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Comment: C: ALL dataset, correct syntax using the exprs call?
... Thanks Martin.   I think my issue revolves around writing the proper syntax to call the required pData (data.frame) and exprs (matrix) elements.  I think I'll need to develop a loop to help me plot the distribution of p-values for gene effect on age (for all 12625 genes). ...
written 4 months ago by detroit.drive0
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ALL dataset, correct syntax using the exprs call?
... Hello - I'm new to the bioconductor suite and still don't quite understand how to invoke the exprs class.  For example, let's say I'm trying to find genes within the ALL dataset with the most and the least significant effect on age.  I've been able to write snippets to find the min/max exprs (expres ...
biobase bioconductor all exprs written 4 months ago by detroit.drive0 • updated 4 months ago by Martin Morgan ♦♦ 22k

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