## User: Daniel Aaen Hansen

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1 month, 3 weeks ago
Joined:
6 years, 8 months ago
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d*****@intomics.com

#### Posts by Daniel Aaen Hansen

<prev • 9 results • page 1 of 1 • next >
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... Hi, I just noticed that the axis labels, title and legend text have gone missing on some of the plots in the quality report. In fact I am not sure which upgrade caused the problem. More specifically, it is the three interactive plots that are missing text labels. The interactive mouse-over text wor ...
written 6.2 years ago by Daniel Aaen Hansen90 • updated 6.2 years ago by Wolfgang Huber13k
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... Dear Wolfgang, I have now been testing the new options for increasing the number of arrays plotted, and I think it is a nice and very useful solution. The only option I lack, is the option to decide how the arrays are sorted. Eg for the spatial plot, arrays could be sorted by name, input order or b ...
written 6.3 years ago by Daniel Aaen Hansen90
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... Dear Wolfgang, The plots are definitely more useful now. Thanks. Regarding implementing an option for plotting all MA-plots and spatial plots, I would suggest a user option 'plot.all' which are false by default to mimic the current behavior. Then in the functions 'aqm.maplot' and 'spatialplot', I ...
written 6.5 years ago by Daniel Aaen Hansen90
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... Dear David and Wolfgang, I had the same problem as David with the PNG plots. I could not run arrayQualityMetrics on a remote server while I was offline (eg. through screen). Doing pdf("dummy.pdf") as suggested (or png("dummy.png")), did not help. The solution for me was to set: > options(bitma ...
written 6.5 years ago by Daniel Aaen Hansen90
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... Dear Wolfgang, I just tested arrayQualityMetrics 3.11.4 on 'MAList' objects and it is working for me (it generates a report). However, I am not sure I understand what is going on. From the box plot and density plot it looks like it is using data that are not log transformed as some expression value ...
written 6.5 years ago by Daniel Aaen Hansen90
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... Dear Wolfgang, Thanks for your reply. We updated our cairo graphics library to version 1.10.2 and that solved the problem with the PCA plot such that it is now interactive. I still get all the warnings and the different behavior depending on whether 'affy' or 'arrayQualityMetrics' is loaded first ( ...
written 6.5 years ago by Daniel Aaen Hansen90
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... Dear Wolfgang and David, I also get more than 50 warnings when I use arrayQualityMetrics. Most of the warnings are of the type: 1: In grid.Call.graphics(L_rect, x$x, x$y, x$width, x$height, ... : X11 protocol error: BadMatch (invalid parameter attributes) But there are also some others (two of ...
written 6.5 years ago by Daniel Aaen Hansen90
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... Dear List, I have a question regarding what weighting function to use when analyzing Agilent data with limma. My question is whether or not it makes sense to down-weight the control probes? I have defined a weighting function: wtfun.Agilent = function(x) { okPopnOutlier = x[,"rIsFeatPo ...
written 6.7 years ago by Daniel Aaen Hansen90
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... Dear Stephen, I have a similar situation and my approach has been to use avereps() from the limma package to average repeated probes. Then I use the biomaRt package to retrieve Ensembl's mapping for the probes since this is being updated with every new release of Ensembl. That should ensure a more ...
written 6.7 years ago by Daniel Aaen Hansen90

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