User: Benjamin Otto

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Benjamin Otto830
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Posts by Benjamin Otto

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Updated affy package? ReadAffy/ AffyBatch has changed and breaks my pipeline!
... Hi Benjamin, Jim, Martin, Is this problem sorted out already? I seem to have the same/similar problem with a code that has been working under R 2.12 and now breaks under 2.14. However I do use the standard human HG-U133-Plus2 package, so I don't think it's a non-Bioc-package problem. Rather I suppo ...
cancer cdf probe affy gcrma annotationdbi written 7.6 years ago by Benjamin Otto830
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R/Bioconductor CDF to Affymetrix CDF
... Dear Colleagues, has someone an idea how I can convert a CDF file in R/Bioconductor format easily into a Affymetrix (Gene expression console compatible) CDF file format? Best regards Benjamin ___________________________________________ Benjamin Otto, PhD University Medical Center Hamburg-Eppendo ...
cdf convert written 8.0 years ago by Benjamin Otto830 • updated 8.0 years ago by Benjamin Otto10
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AffyProbeMiner Mouse 4302 geneccds CDF file
... Dear Bioconductors, we have processed some of our mouse data that we would like to publish with the AffyProbeMiner CDF files (version for R/Bioconductor). For matters of completeness we need not only the R/Boconductor version (that I have) but the GCOS/Expression console version of the "mouse 4302 ...
cdf written 8.4 years ago by Benjamin Otto830
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Answer: A: Unambiguously mapping of affy IDs to gene symbols using hgu133plus2.db
... Hi Christian, that's interesting, I remember that I used to fumble around a little bit when using these annotation packages because of the multiple mappings for some of the IDs. Maybe the way these multiple hits are treated has changed in last versions of the db packages. However, here are two poin ...
written 9.1 years ago by Benjamin Otto830
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Bootstrapping paired samples and tiny groups
... Hi guys, in principle the problem is how to compute a statistic for ultra-tiny group sizes with paired samples. Here is the Model: ------------------------- Assumption 1: A data set of microarrays consists of four classes describing the disease phenotype: type 1, type 2, type 3 and control grou ...
assign written 9.1 years ago by Benjamin Otto830 • updated 9.1 years ago by Naomi Altman6.0k
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Answer: A: Error in Heatmap: Could not find function "heatmap.2"
... Hi Samantha, try the command sessionInfo() and check wether the "gplots" package is loaded. If not, then load it our self. This package should contain the heatmap.2. cheers Benjamin Am 27.07.2010 um 10:56 schrieb Samantha England: > To the Bioconductor Community > > Dear All, > &g ...
written 9.2 years ago by Benjamin Otto830
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Comment: C: problem about hgu133plus2 annotation
... Hi Gina, I do agree with Jim, have a look at the mentioned packages. However if for some reason you still want to use the csv file from affy, do have a look the the merge() function. That should solve your problem. By the way, which one has 54630 rows and which 54640? Because if you use the affy c ...
written 9.2 years ago by Benjamin Otto830
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Comment: C: Heatmap.2 scale problems: Sacling inside the function gives different results th
... Hi Guys, thanks for confirmation. :-) I was pretty sure because I have a little modified script of heatmap.2() where I added some features such as scaling "before" clustering where I can choose between z-score or just median centering, or having the signal color legend below or beside the heatmap ...
written 9.2 years ago by Benjamin Otto830
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Comment: C: Heatmap.2 scale problems: Sacling inside the function gives different results th
... Hi Guys, do note that the scale() function in heatmap doesn't scale your values till AFTER clustering for visualization purpose! So if you provide already scaled data, you naturally will expect a different result. cheers Benjamin Am 22.07.2010 um 16:25 schrieb Bazeley, Peter: > Hi Elmer, > ...
written 9.2 years ago by Benjamin Otto830
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Answer: A: Cross Platform Array Mapping
... Hi David, try BioMart. There is a biocon package for it or you can use the web interface on the ensemble webpage. regards Benjamin Am 10.06.2010 um 16:05 schrieb David Lyon: > Hi > > if I had some human chip array results eg: > http://bioconductor.org/packages/2.6/data/annotation/h ...
written 9.4 years ago by Benjamin Otto830

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Popular Question 7.6 years ago, created a question with more than 1,000 views. For p.adjust returns one uniform value

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