User: Holger Schwender

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Posts by Holger Schwender

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Comment: C: Linkage Disequilibrium Analysis
... Or have a look at the functions getLD and getLDlarge from the trio package also available on CRAN, which can be used to compute LD values genome-wide. You can also plot the LD matrix, and estimate LD blocks using the function findLDblocks. These functions cannot only be applied to trio data, but wer ...
written 6.9 years ago by Holger Schwender900
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Comment: C: Siggenes SAM analysis: log2 transformation and Understanding output
... Hi Jim, hi David, thanks a lot, Jim, for answering these questions. Just one or two comments: > > Lastly, is there an option to specify a FDR threshold? I am running > > through multiple data sets, and I would like to automate it, instead > > of having to looking at a table for e ...
written 7.3 years ago by Holger Schwender900
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Answer: A: siggenes parameters
... Hi Assa, siggenes is described in http://cran.r-project.org/doc/Rnews/Rnews_2006-5.pdf on pages 45ff, and with a bit more technical details in https://eldorado.tu- dortmund.de/bitstream/2003/23306/1/diss_schwender.pdf Section 6.3.2. Another possibility is to look into the code for sam, in parti ...
written 7.9 years ago by Holger Schwender900
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Answer: A: RMA (affy) followed by SAM (samr)
... The SAM implementation in the R package siggenes (which will usually lead to slightly different results than the implementation in samr) can handle ExpressionSet objects. However, just one ExpressionSet object so that you either need to preprocess all cel-files at once or use the exprs function do ...
written 8.0 years ago by Holger Schwender900
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Answer: C: lmFit only deals with numerical values (data matrix object)?
... Numeric values do not necessarily need to be positive. They can also be negative. So you can use your log2 ratios as they are (no matter whether they are positive or negative). Holger ...
written 8.1 years ago by Holger Schwender900 • updated 4.4 years ago by Gordon Smyth37k
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Answer: A: siggenes sam2excel Error
... Does the analysis work if you use > sumis.names = read.table("sumis.names", header=TRUE, stringsAsFactors=FALSE) If not, then I will have a look on this tomorrow. Holger -------- Original-Nachricht -------- > Datum: Wed, 6 Apr 2011 09:37:39 -0700 (PDT) > Von: joseph > An: Holger Sch ...
written 8.1 years ago by Holger Schwender900
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Answer: A: siggenes sam2excel Error
... Hi Joseph, I have just tested sam2excel against several situations which might cause this error. But it works perfectly for me. So without seeing your R code and your data, I actually have no idea why you get this error. Best, Holger -------- Original-Nachricht -------- > Datum: Tue, 5 Apr 20 ...
written 8.1 years ago by Holger Schwender900
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Answer: A: prepare data matrix for siggenes
... siggenes does not care about how you call the columns of your matrix. So both sam and ebam should work. Holger -------- Original-Nachricht -------- > Datum: Mon, 4 Apr 2011 10:57:11 -0700 (PDT) > Von: joseph > An: bioconductor at r-project.org > Betreff: [BioC] prepare data matrix fo ...
written 8.1 years ago by Holger Schwender900
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Answer: A: SAM results
... Hi Michal, the d-values are the values of the moderated t-statistic (called d-statistic in the Tusher paper about SAM). The q-values are the FDR adjusted p-values as proposed by John Storey. And so yes, you can (and actually should if you wanna use them) adjust the raw p-values with any multiple co ...
written 8.5 years ago by Holger Schwender900
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Answer: A: selection of dif.exp.genes defining FDR in SAM
... If you use the R package siggenes, the function findDelta does the trick. Best, Holger -------- Original-Nachricht -------- > Datum: Mon, 21 Jun 2010 17:14:26 +0100 > Von: "Hernando Mart?nez" > An: Bioconductor at stat.math.ethz.ch > Betreff: [BioC] selection of dif.exp.genes definin ...
written 8.9 years ago by Holger Schwender900

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