User: detroit.drive

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Posts by detroit.drive

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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 3 days 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 3 days ago by detroit.drive0 • updated 3 days ago by Gordon Smyth34k
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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 5 days 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 9 days 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 9 days 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 10 days 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 10 days 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 12 days ago by detroit.drive0 • updated 11 days ago by Martin Morgan ♦♦ 22k
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Comment: C: aaMap Import "Not Available"
... Thank you - for some reason I started to think the aaMap as a package similar to the ALL pkg.   ...
written 12 days ago by detroit.drive0
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aaMap Import "Not Available"
...   Hello, I'm experiencing an issue when trying to install the "aaMap" package with its dependencies.  This is exactly what I did, first the Biobase import, then aaMap but I keep getting the Warning message?  I've pasted my sequence below: > biocLite("Biobase") BioC_mirror: https://bioconduct ...
biobase bioconductor aamap written 15 days ago by detroit.drive0 • updated 15 days ago by rreck20

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