User: Joern Toedling

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Posts by Joern Toedling

<prev • 72 results • page 1 of 8 • next >
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Answer: A: GOstats Annotation Package
... Hello, there are functions in the AnnotationDbi package for building custom ".db" annotation packages. See the vignette "SQLForge" in that package for details. This functionality is meant to supersede the AnnBuilder package, which could be used to generate annotation package of the previous generat ...
written 10.2 years ago by Joern Toedling720
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Answer: A: chipAlongChrom problem in Ringo
... Hi Jianping, I presume you created the histogram as we specified in the PLoS CB tutorial article. The error message literally means that the object "y0" does not exist, and you need to create it before drawing the histogram. One option for creating y0, which is the variable holding the threshold f ...
written 10.2 years ago by Joern Toedling720
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Comment: C: chipAlongChrom problem in Ringo
... Hello, this seems to be the source of the problem. The identifiers of the probes that you remapped are of this form 5313_0084_0040 while in the ExpressionSet they are of the form CHR10FS100018407 Were both these types of identifiers given in your array description file (ndf)? If so, and if there's ...
written 10.3 years ago by Joern Toedling720
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Comment: C: chipAlongChrom problem in Ringo
... Jianping Jin wrote: > table(probeAnno["5.index"] %in% featureNames(X)) > > FALSE > 21152 well, none of the probes seems to be included in the names of the probes on your arrays. How did you create the object "X"? Can you show me the output of str(probeAnno["5.index"]) str(probeAnno["5 ...
written 10.3 years ago by Joern Toedling720
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Answer: A: chipAlongChrom problem in Ringo
... Hello, are the warning messages any indication what the source of the problem might be? Does the probeAnno object that you use really correspond to the microarray platform of your ExpressionSet "X"? Maybe you accidentally used a probeAnno from another array platform. Are there actually any probes m ...
written 10.3 years ago by Joern Toedling720
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Comment: C: RinGO problem
... Hi Jianping, the problem turned indeed out to be a change in the Exonerate output file format. Now match start coordinates can be higher than the end coordinate if the match is on the minus strand, while previously in this case the output file would only contain the indication that the reverse comp ...
written 10.3 years ago by Joern Toedling720
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Comment: C: RinGO problem
... Hello, well, the culprit(s) is/are the matches with a negative entry in LENGTH, as these are not supposed to happen. I am not sure how these came about, but it might have to do with changes in Exonerate (the scripts were written for Exonerate version 2.0.0). I shall investigate this further and ge ...
written 10.3 years ago by Joern Toedling720
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Answer: A: RinGO problem
... Hi Jianping, I am not completely sure what the source of the error is yet, so bear with me as I am trying to find out. First, something could be wrong with the merged Exonerate output file. Which version of Exonerate are you using? Can you also please tell me what the output of summary(allchranno ...
written 10.3 years ago by Joern Toedling720
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Answer: A: Installing "lumi" package failure
... Hello Gundula, this might be a problem of conflicting package versions. I presume that this line indicates that some Bioconductor packages are older versions matching the outdated R-2.6 > argument 'lib' is missing: using > '/home/gundala/R/x86_64-pc-linux-gnu-library/2.6' To make sure tha ...
written 10.3 years ago by Joern Toedling720
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Answer: A: Image function
... Hi Priscila, I am not completely sure what kinds of plots you want to generate, but you may want to have a look at the "image.RGList" function in package Ringo and, more general, at the package arrayQualityMetrics which generates diverse sets of plots for quality assessment of microarray data. Plea ...
written 10.3 years ago by Joern Toedling720

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