User: Ulrike Goebel

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Ulrike Goebel110
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11 years, 6 months ago
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u******@mpiz-koeln.mpg.de

Posts by Ulrike Goebel

<prev • 11 results • page 1 of 2 • next >
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Answer: A: New package to identify differentially expressed genes from RNA-seq data
... Hi Likun, Likun Wang wrote: > Dear Ulrike, > > Are there invalid values in your gene expression file? That was it ! Some very high expression values had ","s introduces by Excel to separate the powers of thousand. After removing the commas, it works fine. Seems to be a nice package ! Be ...
written 9.9 years ago by Ulrike Goebel110
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Answer: A: Merging RandData object with names on the IRanges part
... Sorry, I guess this was a clash with the old version that was still installed. After removing it, and also removing all .Rnw files from the /doc directory, I could build and install it. And now the rbind works ! Have a nice weekend Ulrike Ulrike Goebel wrote: > Hi Patrick, > > just t ...
written 10.1 years ago by Ulrike Goebel110
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Answer: A: Merging RandData object with names on the IRanges part
... Thanks a lot for all your suggestions/help ! I will have a look at Rsamtools (I was already wondering whether something like this exists), and, yes, maybe it is really not necessary to read the file in chunks. Thanks again ! Ulrike Ulrike Goebel wrote: > Dear list, > > I would like to do ...
written 10.1 years ago by Ulrike Goebel110
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Merging RandData object with names on the IRanges part
... Dear list, I would like to do the following: Read an output file of BWA (SAM format) in "chunks" and incrementally build a RangedData object from the chunks (by 'rbind') . Ultimately that should be used to get the number of reads per annotated transcript/region, but this is not the question here. ...
iranges written 10.1 years ago by Ulrike Goebel110
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Comment: C: Problem with hyperGTest using ath1121501.db
... Hi Marc, well, now I get > summary(hgCondUnder) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "GO:0044085" not found with the same lists and test direction "under". Strange, because this GO term does exist ! Regards, Ulrike Ulrike Goebel schrieb: > Thanks a lot, Marc ...
written 10.4 years ago by Ulrike Goebel110
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Answer: A: Problem with hyperGTest using ath1121501.db
... Thanks a lot, Marc -- it works now ! Ulrike mcarlson at fhcrc.org schrieb: > Hi Ulrike, > > Thanks for pointing this out. I have just updated this package for > you. Please try out the ath1121501.db_2.2.12.tar.gz version and let > me know if you have any other problems with it. &g ...
written 10.4 years ago by Ulrike Goebel110
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Problem with hyperGTest using ath1121501.db
... Dear list, I seem to have a problem with an obsolote GO id in ath1121501.db. >paramsCondOver <- new("GOHyperGParams", geneIds=H3K27me3_BP, universeGeneIds=uBP, annotation="ath1121501.db", ontology="BP", pvalueCutoff=hgCutoff, conditional=TRUE, testDirection="over") ; >hgCondOver <- ...
annotation go ath1121501 written 10.4 years ago by Ulrike Goebel110
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Answer: A: limma background correction
... Hi Henrique, I recently got the same error with a Nimblegen dataset. Because in this dataset the background is actually not provided (the corresponding column is all-zero), I figured that was the reason ... However, this error occurs only with R-2.7.0, not with 2.6 or 2.5. So something must have ch ...
written 11.2 years ago by Ulrike Goebel110
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Comment: C: Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0
... sorry, I forgot to CC to the list .. ---------- Forwarded Message ---------- Subject: Re: [BioC] Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0 Date: Friday 04 July 2008 11:00 From: Ulrike Goebel To: Joern Toedling Hi Joern, thanks for your suggestion .. but this didn't hel ...
written 11.2 years ago by Ulrike Goebel110
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Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0
... Dear list, I find that I cannot normalize one (of several) NimbleGen files in R-2.7.0 (using the preprocess() function of package Ringo), while I did normalize this dataset successfully before with R-2.5.0. I guess this is not even a problem of Ringo, but rather of normalizeWithinArrays (and thus ...
probe annotate geneplotter affy vsn ringo written 11.2 years ago by Ulrike Goebel110 • updated 11.2 years ago by Joern Toedling720

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