User: Samuel Wuest

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Samuel Wuest330
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Posts by Samuel Wuest

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problems with annotation package (error in AnnotationDbi v1.18.1 ?)
... Hi all, I have a problem that concerns the use of annotation packages, here in an example for a custom-made AGILENT microarray for Arabidopsis (but I think it also concerns the org.At.tair.db package). I don't quite understand how this issue arises, so sorry for the vague title (my guess is that it ...
microarray annotation annotationdbi written 7.5 years ago by Samuel Wuest330 • updated 7.5 years ago by Marc Carlson7.2k
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Answer: A: Summarizing two-channel data (RGList, MAList) for limma analysis
... Hi Stephen, one option is to simply average multiple probes matching to the same transcript, using the avereps()-function (from the limma package). It takes an ID-argument, where you specify the transcipt (or maybe even "locus")-names, so that probes with the same IDs will be averaged. If you have ...
written 7.9 years ago by Samuel Wuest330
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GenomeGraphs plots: polygon tracks for sequencing coverage data
... Hi, I think the GenomeGraphs package is very handy to visualize genomics data; however, I am trying to find a way to represent sequencing coverage (e.g. ChipSeq) as polygon, as seen for example in the GBrowse- visualizations. I have used the makeBaseTrack-function to visualize per-base coverage, ...
sequencing coverage visualization genomegraphs written 8.0 years ago by Samuel Wuest330
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Answer: A: Two channel data vs. one colour data for PCA, heatmaps and clustering
... Hi John, I would also recommend using the limma package for your type of analysis. After appropriate normalizations/bg-corrections, you can extract log-intensities from an MAList object using the exprs.MA() function. This will return a matrix object that you can use for pca/heatmaps as you've used ...
written 8.1 years ago by Samuel Wuest330
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Comment: C: biomaRt query problems- plants_mart_10
... Oh, I am sorry, haven't seen the announcement. My queries are working again, so back to normal. Thanks a lot! Sam On 23 October 2011 22:32, Dan Tenenbaum wrote: > On Sun, Oct 23, 2011 at 2:27 PM, Wolfgang Huber wrote: >> Dear Sam >> >> I have just run your script, and it s ...
written 8.1 years ago by Samuel Wuest330
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biomaRt query problems- plants_mart_10
... Hi, I have tried to use biomaRt (primarily for use in the GenomeGraphs-package) to retrieve data from the pants_mart_10 -Mart, and it seems that the service is unstable at the moment (that is, it works in times but not others). I observed the problem firstly two days ago and I have not been able to ...
biomart written 8.1 years ago by Samuel Wuest330 • updated 8.1 years ago by Wolfgang Huber13k
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Comment: C: R/Bioconductor CDF to Affymetrix CDF
... Hi Benjamin, I would agree with the answer given below, but would like to add that - as far as I recall - a similar post has already been discussed before, https://stat.ethz.ch/pipermail/bioconductor/2008-December/025647.html If you really have to coerce the data into the list-structure that Jim ...
written 8.2 years ago by Samuel Wuest330
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Answer: A: help to proceed with the interpretation of an analysis
... Dear Alberto, I am not quite sure how your experimental design looks like in detail, but it seems to me that you have dual-label microarray data and an unconnected design with two factors (hence the two separate comparison?). If this is the case, then there is a very nice functionality in the limma ...
written 8.4 years ago by Samuel Wuest330
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PICS: vignette code outdated (use of GenomeData-object)
... Hello, I am trying to follow the example outlined in the PICS vignette in order to analyse a ChIP-Seq dataset, but the code does not actually work anymore (see code below). The GenomeData-object used for the analysis (i.e. the segmentReads-command) cannot be constructed anymore, it seems that the ...
convert pics written 8.6 years ago by Samuel Wuest330 • updated 8.6 years ago by Valerie Obenchain6.7k
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Answer: A: pa.calls-function in package "panp"
... Hi Kyle, as far as my original post is concerned: there was a small bug in the approxfun-function used by pa.calls in R 2.11.X, and the problem has been fixed after R 2.11.1. I am using R 2.12 now, and there are no further problems. See also: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14 ...
written 8.6 years ago by Samuel Wuest330

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