User: detroit.drive

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Posts by detroit.drive

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Comment: C: RNA-Seq Workflow Example (not "airway") for R
... It appears that the 'fission' package is very similar to 'airway'. Is it possible to follow the workflow steps posted on the web for airway but replace the data with fission? ...
written 3 months ago by detroit.drive0
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Comment: C: RNA-Seq Workflow Example (not "airway") for R
... Many thanks Gordon. The bottom three links are just what I was seeking. V/r, DD ...
written 3 months ago by detroit.drive0
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RNA-Seq Workflow Example (not "airway") for R
... Hi Everyone, It seems like every example (on the web) for an RNA-Seq workflow uses the "airway" dataset. Does anyone know of a Bioconductor RNA-Seq workflow example that's something other than airway? Very respectfully, DD ...
rna-seq workflow written 3 months ago by detroit.drive0 • updated 3 months ago by Gordon Smyth38k
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facsDorit package: Error in file(filename, open = "rb") : cannot open the connection
... Hi everyone, I'm following the pipeline for processing and visualizing data from high throughput cell-based assays directly from "Bioinformatics and Computational Biology Solutions Using R and Bioconductor" (pg. 78). I'm trying to read in the FCS data using their suggested code but keep getting the ...
facsdorit readcytoset written 5 months ago by detroit.drive0
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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 9 months ago by detroit.drive0 • updated 9 months ago by nhejazi0
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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 12 months ago by detroit.drive0 • updated 12 months ago by James W. MacDonald51k
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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 13 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 13 months ago by detroit.drive0 • updated 13 months ago by Gordon Smyth38k
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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 13 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 13 months ago by detroit.drive0

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