User: Joern Toedling

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Posts by Joern Toedling

<prev • 72 results • page 2 of 8 • next >
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Answer: A: issue of genome build versions when using biomaRt
... Hello, if you use the Ensembl biomart, you get access to the genome builds as they are/were current in that release of Ensembl. For example, in the current Ensembl release (50), it is NCBI36 for H.sapiens. You can see which versions of genome builds are associated with that release by: ensembl < ...
written 11.1 years ago by Joern Toedling720
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Answer: A: At a loss on new project with Affymetrix U133 2.0
... Hello, you might want to have a look at the following packages: - affy: for importing the data and preprocessing - arrayQualityMetrics: for quality assessment of the arrays - hgu133a2.db: for the annotation of the probe sets on the microarray - limma, siggenes: for finding differentially expressed ...
written 11.1 years ago by Joern Toedling720
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Comment: C: tilingArray- normalizeByReference
... Anjan, looking at the source code of the function normalizeByReference, there is indeed the line vsnMatrix(xn, lts.quantile = 0.95, subsample = as.integer(2e+05)) , and since your matrix only has 6488 lines, this cannot work. Without knowing more details about your array platform and study, I cannot ...
written 11.1 years ago by Joern Toedling720
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Answer: A: tilingArray- normalizeByReference
... Hello Anjan, well, the error message indicates that your vector pm_vector is not usable by the function. Is it really an integer vector. What is the output of str(pm_vector) ? Probably, it would be better to read in the file by something like pm_vector <- read.delim("PerfectMatchIndex", skip=)$V ...
written 11.1 years ago by Joern Toedling720
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Answer: A: Nimblegen expression dataset(.xys or.pair files/folders)
... Hello, a mouse expression data set in NimbleGen's ftr format can also be found in the ArrayExpress data base, The experiment data has the identifier E-TABM-183 and the array platform can be found under A-MEXP-607. For converting the ftr into xys files, you can use the function ftr2xys from package " ...
written 11.2 years ago by Joern Toedling720
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Answer: A: Bioconductor installation on 64 bit R problem
... Hi Octavio, looks to me like this is not a Bioconductor issue, but that your R is not working properly as the "methods" package cannot be attached (do you get the same error message, when starting R and typing 'library("methods")'? ). How did you install R? Did you get it from some RPM or other pre ...
written 11.2 years ago by Joern Toedling720
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CEL files of ALL data set
... Hi Willem, I had created an R-Package containing the CEL files from those two studies. You can retrieve it from our local repository. Within R call repUrl <- contrib.url("http://www.ebi.ac.uk/huber-srv/data/Rrepos") install.packages("ALLcelfiles", contriburl=repUrl) Let me know if you encounter ...
arrayexpress written 11.2 years ago by Joern Toedling720
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Answer: A: Question about using Biostrings & BSgenome
... Hello, Biostrings and BSgenome can certainly be used to retrieve genomic sequences. For instance, here's a very basic function I have used many times to retrieve the sequence of short genome segments on either strand of budding yeast. getYeastSeq <- function(chr, start, end, strand="+"){ stop ...
written 11.2 years ago by Joern Toedling720
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Answer: A: object "annFUN.db" not found in topGO
... Hello, there is probably some issue with incompatible package versions, since you seem to be using a very old version of topGO. Please always attach the output of sessionInfo() to your questions to this list. You should the install the newest version of R (R-2.7.2) and then update all used packages ...
written 11.3 years ago by Joern Toedling720
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Answer: A: GO over representation analysis
... Hello, I was quite happy with the package topGO, which allows you to supply the mapping between gene-identifiers and GO term IDs as a list. Such a list can be easily created using the biomaRt package to query the Ensembl database, or the list can be created from other annotation sources. The topGO v ...
written 11.3 years ago by Joern Toedling720

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