User: StephanieK

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StephanieK90
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Posts by StephanieK

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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... Thank you. So since there are so many different ways to do this analysis, I checked with someone exactly how I should do it, would this make sense to you? I have some data sets: the phenotypic data is different age categories (sometimes two age categories, sometimes >2; the aim is to find DE gene ...
written 3.5 years ago by StephanieK90
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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... Thank you so much. I got advice from someone who knows more than me, and she said: "It's best for the linear model to set the intercept. If you set an intercept you are saying you expect the line to go through the origin (which isn't normally the case for microarray data). Generally the intercept is ...
written 3.5 years ago by StephanieK90
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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... Thanks so much, so I've edited the code slightly to include comments etc for other people to understand, I just have one question: This is the code (for everyone else): library(limma) library(Biobase) #Make an expression data set expr <-as.matrix(read.table("Table.tabbed",h ...
written 3.5 years ago by StephanieK90
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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... I found out how to relevel, finally! I was putting it in the wrong place, for everyone else: add the line f <-relevel(f,"Age2.5") under the line: f <-factor(as.character(exampleSet$Age)) So then if I do that, my output is: Removing intercept from test coefficients ...
written 3.5 years ago by StephanieK90
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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... Thank you so much for your help. I know how to relevel factors, I've done it in the Cox Model before, but I'm actually having trouble with it here. My total code is: library(limma) library(Biobase) expr <-as.matrix(read.table("Table.tabbed",header=TRUE,sep="\t",row.names=1,as.i ...
written 3.5 years ago by StephanieK90
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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... Thanks, I had actually made a small mistake, this is the output (in the previous, I just replaced the gene names with fake names to save space). Can I ask what variable you were looking at that let you know that? The output is now: An object of class "MArrayLM" $coefficients ...
written 3.5 years ago by StephanieK90
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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... Thanks, sorry I have multiple data sets, both with two and more than two age groups. I have switched to limma and posted the input file, the code and the output below, if you had any thoughts I'd appreciate it. ...
written 3.5 years ago by StephanieK90
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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... So can I ask: 1. How could you tell my previous method was underpowered (i.e. from the intercept or age variable?), because I'll need to work out some how how my current model fits the data/is the test is well powered enough, so if you knew where I should be looking to find this info. 2.Do you agre ...
written 3.5 years ago by StephanieK90
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Comment: C: How to tell if a gene is over- or under-expressed from the output of F test (dif
... Thanks. I've switched to limma. I have a gene expression matrix of normalised gene expression values. There is >26,000 genes, start of the file is like this: Gene Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Gene1 5.20 5.05 5.01 4.96 5.31 4.83 Gene2 4.85 4.59 4.91 5.06 4.75 4.86 ...
written 3.5 years ago by StephanieK90
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How to tell if a gene is over- or under-expressed from the output of F test (differential gene expression)?
... Hi all, I have a set of normalised, log2 transformed gene expression data for two age groups. I performed a linear regression on each gene, and used an F test to determine whether the slope of the curve between the two age groups is different than zero, which in this case would indicate that there ...
f test gene R linear regression written 3.5 years ago by StephanieK90 • updated 3.5 years ago by Devon Ryan95k

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Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Learning Python: list of resources

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