User: Joern Toedling

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Posts by Joern Toedling

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Comment: C: multicore Vignette or HowTo??
... Hi Edwin, this has probably been answered already by now, but in case it hasn't: The solution is simple: library("multicore") options("cores"=4) result <- mclapply(, ) No need to create extra vectors or something, mclapply will distribute the computations on each individual object on one pro ...
written 7.1 years ago by Joern Toedling450
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Answer: A: Quantile normalization in Ringo package
... Hi, you can use the 'normalizeBetweenArrays' function from package limma with method="quantile" on your RGList and then convert the resulting MAList using the function asExprSet from the Ringo package. Please check the source code of "preprocess", as it does the same thing for other methods. So it' ...
written 7.1 years ago by Joern Toedling450
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Comment: C: Error mapping RNA-seq data to genome
... Hello, as the mtDNA is circular, such an overhanging alignment covering end and start of the mtDNA is not worrying at all. As such an alignment can also happen with bacterial genomes, one could start thinking whether such alignments should be treated in a special way. However, I am not sure whethe ...
written 7.2 years ago by Joern Toedling450
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Answer: A: using smoothX in Ringo
... Hi Lizzy, thanks for sending me these. I am still puzzled by the error message, but I think the problem are the factor-vectors in your probeAnno PA. The "index" components are assumed to be either character vectors that correspond to the featureNames of X or integer vectors corresponding to row num ...
written 7.3 years ago by Joern Toedling450
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Answer: A: using smoothX in Ringo
... Hi Lizzy, I think you are right and there might be a small issue with the objects that you created. How exactly did you create them? First check if the argument 'modColumn' is set correctly. What is the output of str(X$Cy5) Alternatively, the probeAnno could be the culprit. What are the results of ...
written 7.3 years ago by Joern Toedling450
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Answer: A: Accessing attributes of object
... Hi, this is not really a Bioconductor question and should have been asked on the more general R-help list. Nevertheless, the answer is given on the help page of TukeyHSD. Each element of the result list is a matrix and can be accessed accordingly. So tuk.dat$disease[1,1] will return the first ele ...
written 7.3 years ago by Joern Toedling450
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Answer: A: Ringo and dye swaps
... Hello, using the targets file to indicate dye-swaps is a nice idea, but unfortunately Ringo currently cannot understand this. The values that Ringo works with in later steps are always the ratios ChIP/input and they are assumed to correspond to the separate channels. So when calling "preprocess" o ...
written 7.3 years ago by Joern Toedling450
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Answer: A: Nimblegen 385K CpG Island Plus Promoter Arrays
... Hello, I'm afraid you need to provide us with more details in order for us to tell you which Bioconductor package might be able to do a better job than your not-so-good superhero. For example, for looking at ChIP-chip experiments on NimbleGen arrays you can have a look at the Ringo package. For Me ...
written 7.4 years ago by Joern Toedling450
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Answer: A: get table with aanotaed genome features
... Hi Andreia, please have a look at section 2.8 of the girafe vignette. The resulting object from interval_overlap(A,B) is a list of the same length as A with the i-th list element being the indices of B that overlap A[i]. Generating a character vector of overlapping RNA types can be done with 'sap ...
written 7.4 years ago by Joern Toedling450
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Answer: A: R package modreg
... Hello, in the future, please use the R-help list for such general questions rather than this list, which is reserved for Bioconductor-related questions. Anyway, it seems that the package 'modreg' has been merged into 'stats' a long time ago (R-1.9.0), so you may want to check out the 'loess' funct ...
written 7.4 years ago by Joern Toedling450

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