User: Tobias Straub

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Tobias Straub410
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Posts by Tobias Straub

<prev • 41 results • page 1 of 5 • next >
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Answer: A: Advise on setting up a non-specific filter for differential expression
... Hi Wolfgang, just an experience. in some of my analyses applying variance filtering resulted in problems fitting N(0,1) to the limma t statistic. now that i had a quick look at your paper I get an idea that combining limma with the variance filter is anyway not a good idea. the performance of mas ...
written 9.2 years ago by Tobias Straub410
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Answer: A: Advise on setting up a non-specific filter for differential expression
... Hi Lucia! did you already have a look at the nsFilter function in the genefilter package? nsFilter(eset, require.entrez = F, require.symbol = F, require.GOBP = FALSE, require.GOCC = FALSE, require.GOMF = FALSE, remove.dupEntrez = TRUE, var.func = IQR, var.cutoff = 0.5, var.filter = TRUE) would si ...
written 9.2 years ago by Tobias Straub410
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Advise on setting up a non-specific filter for differential expression
... Hi Lucia I am not sure if I completely understand your problem, just want to mention that I routinely apply non-specific filtering based on MAS5 calls with a very good outcome (based on a prior-knowledge training set). I do not like so much the alternative approach - filtering based on variance or ...
qpcr written 9.2 years ago by Tobias Straub410
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Answer: A: Is there a package or a way to convert "probesets" to "genes"
... hi richie, one easy way to handle the multiple probesets per gene problem is to keep only the one probeset with the highest variance across replicates. the 'nsFilter' function in the 'genefilter' package provides this operation for ExpressionSet objects. using this filter approach you might of cour ...
written 9.9 years ago by Tobias Straub410
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Answer: A: Help with Oligo Package: Extracting and Graphing
... Hi Noah, did you contact Benedikt, the author of the Starr package? the department he's working in is performing tiling array analysis in S. cerevisiae (most likely on exactly the same array as yours) and i am pretty sure they can provide not only the proper pd file but also a 'working' gff file. ...
written 9.9 years ago by Tobias Straub410
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Answer: A: Read jpd images and rename, sizing and embed a scale bar
... hi sundar, 1 and 2 should covered by the EBImage package. not sure about 3. you ever considered to do this using bona fide image manipulation tools such as ImageJ (http://rsbweb.nih.gov/ij/)? best tobias On Nov 7, 2009, at 5:10 AM, sundar Venkat wrote: > Dear Users, > I w ...
written 10.0 years ago by Tobias Straub410
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Answer: A: Gene list ideogram
... Hi Dan, it is difficult to come up with a solution that fits everyone's needs. i setup a plot function using the 'grid' package. good thing about grid is that you can easily create viewports with a custom coordinate system. in addition plotting of graphical primitives like boxes (=genes) is accompl ...
written 10.0 years ago by Tobias Straub410
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Comment: C: Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
... Hi On Oct 27, 2009, at 4:13 PM, Massimo Pinto wrote: > Dear Francois, Tobias, and all users > > Thanks to this discussion, and those that I have found on the > Archives, as Francois suggested, I am more aware now of the importance > of avoiding averages of different probes that map ...
written 10.0 years ago by Tobias Straub410
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Answer: A: agi4x44preprocess
... what about >targets = read.targets(infile="infile.txt") >read.AgilentFE(targets, makePLOT) best T. On Oct 27, 2009, at 4:43 PM, Neel Aluru wrote: > Hello, > > I am just beginning to work with Bioconductor and started having > issues, which I think are minor but cannot figure o ...
written 10.0 years ago by Tobias Straub410
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limma normexp background correction bug?
... hi i was playing around with various background correction methods using limma and discovered that whatever normexp.method i call for the "normexp" method, the result is exactly the same. in fact the more i digged into it the more i believe that normexp is not executed at all. looking at the code ...
written 10.0 years ago by Tobias Straub410 • updated 10.0 years ago by Gordon Smyth38k

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