User: Simon Melov

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Simon Melov340
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Posts by Simon Melov

<prev • 34 results • page 1 of 4 • next >
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edgeR outlier question for version 3.0.8
... Hi Gordon, I'm analyzing a fairly large RNAseq data set (N of roughly 20 per group), and wanted to know what changed had been made to the prior as you indiate below from last year. Do we still need to set the prior when looking at comparatively large data sets? Or is edgeR less smoothing in the late ...
rnaseq go edger written 6.2 years ago by Simon Melov340 • updated 6.2 years ago by Gordon Smyth38k
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limma and legacy data
... Hi, I'm trying to do some line plots of genes of interest from a bunch of old microarray data we have (dye-swaps!). I can go through the workflow fine as recommended in the limma guide, however, I'd really like to generate some lineplots of the expression. We have quite a lot of arrays per group, an ...
microarray go graph limma written 6.9 years ago by Simon Melov340
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Comment: C: HTqPCR problems
... Great, thanks Heidi. This did the job. Quick question, can you make scatterplots instead of barcharts for any of the plot functions? I've looked at plotCtOverview, and I dont see a way to specify the chart type. Its helpful to have some flexibility here, so you can see how tight the spread is (perso ...
written 7.1 years ago by Simon Melov340
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Answer: A: HTqPCR problems
... Hi Heidi, I've a followup from the question from listed below. I've started to merge multiple plates together using rbind as you suggested. I've identical gene order per plate, but different biological samples belonging to different groups per plate. I can manipulate these using your graphing functi ...
written 7.1 years ago by Simon Melov340
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Comment: C: HTqPCR plotting groups of interest
... This worked great Heidi, thanks very much! It would be great if you could put this in the next update as an example. When you have a lot of groups, you dont want to plot them on every graph. Also, I think you have the color function set to only plot 10 colors as a default. People might be confused ...
written 7.1 years ago by Simon Melov340
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HTqPCR plotting groups of interest
... If anyone can help, it would be great. I want to plot different groups of interest in HTqPCR using some of the plot functions, and I've played around with plotting different ways a number of times, and cant get the plot functions in HTqPCR to display what I want. I've a large number of groups, and ...
htqpcr written 7.2 years ago by Simon Melov340 • updated 7.1 years ago by Heidi Dvinge2.0k
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Comment: C: HTqPCR problems
... Hi Heidi, I think I've identified the problem. Currently it appears as though HTqPCR reads the sample ID's and genes in from top to bottom of the CSV output from the Biomark. This is not the sample order we load in. As long as thats made clear in the vignette, it will prevent any confusion. We typic ...
written 7.2 years ago by Simon Melov340
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Comment: C: HTqPCR problems
... Hi Heidi, getting there, hopefully if you can clarify the following issue, all will be well and good. After yesterdays correspondence, I'm now producing nice plots, when I check the actual values being plotted, they dont match up to the sample ID's. In fact, if I dont bother assigning groups, the s ...
written 7.2 years ago by Simon Melov340
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Comment: C: HTqPCR problems
... Hi Heidi, you are correct, yes 48.48. The example you provide below is exactly what I needed for clarification for groups. I was trying to reverse engineer what you had done with the original expression set package for microarrays, but from below, I can get this to work now. Just to be clear, I hav ...
written 7.2 years ago by Simon Melov340
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Comment: C: HTqPCR problems
... Thanks for the help Heidi, but I'm still having troubles, your comments on the plotting helped me solve the outputs. But if I want to just display some groups (for example the LO group in the example below), how do I associate a group with multiple samples (ie biological reps)? Currently I'm associ ...
written 7.2 years ago by Simon Melov340

Latest awards to Simon Melov

Popular Question 6.2 years ago, created a question with more than 1,000 views. For Limma Fit - Error: (subscript) logical subscript too long
Popular Question 6.2 years ago, created a question with more than 1,000 views. For edgeR outlier question

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