User: swbarnes2

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swbarnes2200
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Posts by swbarnes2

<prev • 54 results • page 1 of 6 • next >
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Comment: C: how to change PCA plot in ropls
... Is this really a software error? ...
written 7 days ago by swbarnes2200
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Answer: A: DESeq2 Interaction Term Interpretation for Microbiome Data
... For interactions, even though the column is labeled "logFold2Change", that's not what it is. Edit: It's the log of the **ratio** of the fold changes. I found this site helpful https://rpubs.com/ge600/deseq2 Look down to the header "The different response in genotypes (interaction term)" ...
written 7 days ago by swbarnes2200
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Answer: A: DESeq2 log fold change
... > 1) get normalized count (2) log transformation (3) calculate averages > per condition (4) divide two averages: "FC". Is this a right way? No. Take the averages of the normalized counts, divide one by the other, take the log base 2 of that. ...
written 7 days ago by swbarnes2200
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Comment: C: How to add row data to DESeqDataSetFromMatrix
... You need to post the top few lines of your files for anyone to be able to help you. Have you looked at the file formats used in datasets from tutorials, to see how they differ from what you have? ...
written 8 days ago by swbarnes2200
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Does response on subset of data in DESeq
... Lets say I have an experiment like this (assume every sample has replicates) treatment control control Treatment1 Treatment1 Treatment2 Treatment2 If I wanted to compare Treatment 1 to control, I'd likely make the dds object with **all the samples**, and use contrast ...
deseq2 written 18 days ago by swbarnes2200 • updated 15 days ago by Michael Love24k
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Answer: A: Intercept result in DESeq2 two factor model
... > From what I understand the results are telling me that there is a gene > expression difference between species 1 and species 2 without > accounting for treatment state, a difference between treatment 1 and > untreated control and treatment2 and untreated control without > accounting ...
written 18 days ago by swbarnes2200
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Answer: A: DESeq2 logfoldchange and interaction in model
... For interaction tests, the column is labeled "LogFoldChange", but it really is a ratio of fold changes. You can eyeball this yourself by using the normalized counts, and working out the average values of the different treatments, and comparing their ratios. The number will not quite match what DES ...
written 20 days ago by swbarnes2200
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Answer: C: Principal components in DESeq2
... intgroup.df isn't doing anything there. I like to throw in `pca_merged <- merge(colData(dds), pca$x, by.x = 0, by.y = 0)` to get all the info in one place. ...
written 25 days ago by swbarnes2200
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Answer: A: Creating an Expression Set from a csv file or EXCEL file
... edata = read.csv(file="C:\Users\Owner\Dropbox\LouiseShoweProjects\lung cancer mRNA and miRNA\c.prevsn.pre\c.prevsn.pre.csv", header=TRUE, sep=",") For starters...no spaces in folder names, ever. ...
written 28 days ago by swbarnes2200
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Comment: C: How to subset data
... You need to walk through the example from the vignette, because you aren't following the example at all. ...
written 29 days ago by swbarnes2200

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