User: Jahn Davik

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Jahn Davik110
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Posts by Jahn Davik

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Comment: C: exporting limma log2 data
... It helps. Thank you so much for the feedback. jd     ...
written 3.1 years ago by Jahn Davik110
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Comment: C: exporting limma log2 data
... Dear MacDonald, Thanks for the reply. I wanted to extract the data in order to do boxplots of probes of my interest. But if that is possible within limma, advice is greatly appreciated.   jd   ...
written 3.1 years ago by Jahn Davik110
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exporting limma log2 data
... Dear all, I am quite new to limma and need to ask how to export the normalized data. I want to use them in graphical data exploration and presenatation. So, I do something like this (following the Mattick Lab post): library(limma) targets <- readTargets('targets.txt') x <- read.maimages(t ...
limma export log2 data agilent written 3.1 years ago by Jahn Davik110 • updated 3.1 years ago by James W. MacDonald45k
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Comment: C: edgeR factorial experiment contrasts
... Hi Jim, Thank you for the thorough feedback. Appreciate it. Best jahn Fra: James W. MacDonald [mailto:jmacdon at uw.edu] Sendt: 4. september 2014 16:40 Til: Jahn Davik Kopi: Jahn Davik [guest]; bioconductor at r-project.org Emne: Re: [BioC] edgeR factorial experiment contrasts Hi Jahn, On Thu, ...
written 3.2 years ago by Jahn Davik110
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Comment: C: edgeR factorial experiment contrasts
... Hi Jim, Thanks for clarification. Appreciate it. For the sake of it I ran a couple of comparisons between the one-way approach that you advocate and the factorial approach. For the simple comparisons, e.g., E00 vs J00, the two approaches returned pretty much the same results. When I did the compari ...
written 3.2 years ago by Jahn Davik110
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Comment: C: edgeR factorial experiment contrasts
... Moreover Jim, And also: what about the interactions? I guess that was one of my issues when I tried to think in traditional factorial terms. To account for them, I mean. But again: I'm in unknown waters here. jahn ________________________________________ Fra: bioconductor-bounces at r-project.org [ ...
written 3.2 years ago by Jahn Davik110
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Comment: C: edgeR factorial experiment contrasts
... Hi Jim, Yes, I believe I can see that (except for possibly my third question). It's just that I tend to think along these lines. Are they wrong? jahn ________________________________ Fra: James W. MacDonald [jmacdon at uw.edu] Sendt: 3. september 2014 22:06 Til: Jahn Davik [guest] Kopi: bioconduct ...
written 3.2 years ago by Jahn Davik110
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Comment: C: edgeR
... Smashing! Thanks. jahn -----Opprinnelig melding----- Fra: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] Sendt: 8. april 2014 10:02 Til: Jahn Davik Kopi: Bioconductor mailing list Emne: Re: edgeR Yes. If you want transcripts that are up in contrast1 and down in contrast2: selected <- (dt1&g ...
written 3.6 years ago by Jahn Davik110
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Comment: C: edgeR
... Great! Thank you. That worked well. An additional one: Can you in this framework filter out the DE transcripts with a particular direction? E.g., if I wanted only the one with higher counts in one of the elements from lrt1? I have done that using the logFC (and exact tests), but I am not able to see ...
written 3.6 years ago by Jahn Davik110
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Comment: C: edgeR
... Gordon, Don't worry about my last request. Looking closer into your User's Guide (e.g., section 3.3 ), I believe you actually have addressed these issues. Sorry for the hassle. Best jahn ...
written 3.8 years ago by Jahn Davik110 • updated 2.8 years ago by Gordon Smyth32k

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For exporting limma log2 data

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