User: StephK

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StephK70
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Posts by StephK

<prev • 10 results • page 1 of 1 • next >
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Comment: C: F test for two phenotypic and multiple phenotypic categories.
... Thank you so much. Can I ask, regarding the F test, you can see from my above code that for the two-age test, I get a T test p value and for the more-than-two age category, I get a two-tailed F test p value. I understand that the T and F test are related; I'm wondering if it's possible to obtain a t ...
written 2.2 years ago by StephK70
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F test for two phenotypic and multiple phenotypic categories.
... Dear all, I have some gene expression data sets. In some of the data sets, I am comparing two age categories, and in some I am comparing multiple age categories. For each dataset, I want to do a two-tailed F test between the age categories to check if the slope of the curve is different from zero, ...
limma differential gene expression f test written 2.2 years ago by StephK70 • updated 2.2 years ago by Ryan C. Thompson7.1k
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Algorithm for between and within microarray normalisation (for meta-analysis).
... I apologise if this is not the right place to ask, please advise. The aim of my experiment is to look at healthy ageing gene expression changes. Thus, I want all of the data sets from GEO that studied gene expression at different ages (either comparing young to old, or as a time series), and then I ...
microarray meta-analysis gene expression written 2.5 years ago by StephK70 • updated 9 days ago by Bioconductor Community ♦♦ 0
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Comment: C: plotting a CA
... May I please pick your brain once more! I used the code you sent and modified it slightly but i just need help with one part, also i appreciate the reading you sent (to Ms. Culhane)...... so I've highlighted the awkward part in yellow, but i've sent the full code so as to provide context: #### In ...
written 6.9 years ago by StephK70
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Comment: C: plotting a ca.
... Hmm. I didn't have this error on my smaller dataset, but i get the same thing when i use a bigger dataset. So far, I know all i know is what the error tells me, it has something to do with the way i am reading in the "interesting" nodes that i want to highlight. I have been looking at this page: ...
written 6.9 years ago by StephK70
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Answer: A: plotting a ca.
... I can't help you yet because i am only learning it now myself, but have you seen the intro pdf on the made4 page? http://www.bioinf.ucd.ie/people/aedin/R/ On Sat, Mar 10, 2012 at 5:08 PM, Aaral Singh wrote: > Hello. I have followed conversation re:plotting a ca. > > Have try with data ...
written 6.9 years ago by StephK70
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Comment: C: plotting a CA
... Thank you. I tried to modify it slightly. It did not go well. At this step: creating a group of interesting nodes: fac<-factor(c(rep("Node1",3), rep("Node2", 2))) In reality there can be hundreds of these nodes. So instead of typing the nodes in manually, i wanted to read the nodes in from a fi ...
written 6.9 years ago by StephK70
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Comment: C: plotting a CA
... O wow i was way off. Many thanks. May i ask one question (I'm a total newbie), i was trying out the different pieces of (much appreciated) code because i want to play around with them and make sure i understand them. But i have never used a function in R. For this section: xax =1, yax = 2, .. o ...
written 6.9 years ago by StephK70
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Comment: C: plotting a CA
... I still appreciate that you took the time to read. Many thanks! On Thu, Mar 8, 2012 at 6:08 PM, Tim Triche, Jr. wrote: > Disregard what I said, although the paper may still be of interest. I > misunderstood what you wrote. > > Apologies to all involved. > > --t > > > On ...
written 6.9 years ago by StephK70
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Comment: C: plotting a CA
... Many thanks. I tried this: table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1", "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2", "codon3"))) library(ca) plot(ca(table,suprow=c(4,5))) This will give me a ...
written 6.9 years ago by StephK70

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