User: Maxim

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Maxim170
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Posts by Maxim

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Comment: C: Gviz: axes related parameters
... Hi, thanks for the information, the plot suggested by you is exactly what I have right now! Actually I like the plots that I was able to produce with Gviz a lot. http://postimg.org/image/u9cs7014f/ The code was produced using a wrapper function, the relevant part producing the DataTracks looks li ...
written 5.6 years ago by Maxim170
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Comment: C: Gviz: axes related parameters
... Hi, sorry, you're of course right, my question not phrased correctly. I didn't mean "cut", rather cross, better intersect, i.e. a typical coordinate system, where x and y intersect at coordinate (0,0), e.g.: http://en.wikipedia.org/wiki/File:Cartesian-coordinate-system.svg (of course without negat ...
written 5.6 years ago by Maxim170
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Gviz: axes related parameters
... Hi, since very recently I'm using Gviz for plotting coverage vectors from ChIP-seq data. I would like to stick to it as it draws gene models much nicer than my previous attempts drawing them with my own plotting functions. I wonder whether it is possible to have mountain/polygon or histogram tracks ...
coverage gviz written 5.6 years ago by Maxim170 • updated 5.7 years ago by Steve Lianoglou12k
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Comment: C: mogene10stprobeset.db error
... Good to hear about this! This is actually my first 1.0 st gene chip analysis, before I just did classical 3'-IVT arrays. Despite of the fact, that the aroma manuals I was able to find perhaps may not be as comprehensive as for the limma/affy packages I still was surprised to get my array results in ...
written 9.3 years ago by Maxim170
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mogene10stprobeset.db error
... Hi, I try to analyze MoGene-1_0-st gene arrays. I used the aroma package to do this and came up with an expression matrix, but have no clue, how to assign real gene names to the respective "IDs" (column "item numbers" after aroma normalization and summarization). As a workaround I simply tried to ...
normalization assign written 9.3 years ago by Maxim170 • updated 9.3 years ago by Vincent J. Carey, Jr.6.3k
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vennSelect problem with hgu133plus package
... Hi, I have a problem to understand what I type of variables I have to feed into the function vennSelect. As the vennDiagram is only able to get the overlap between multiple contrasts depending on the p.value (btw: can I use the decideTests function dependent on the adj.p.value, too?), I took a loo ...
hgu133plus2 written 9.5 years ago by Maxim170 • updated 9.5 years ago by James W. MacDonald51k
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stuck with affy/ limma
... Hi, thank you, that solved most my problems. But of course this is where new problems arise. Anyhow, this aspect works nicely, thanks for pointing me at the right direction. Best regards Maxim 2010/3/31 James MacDonald > > > Maxim wrote: > >> Hi, >> >> I have a que ...
clustering genefilter affy limma written 9.5 years ago by Maxim170
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stuck with affy/ limma
... Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the geno ...
clustering affy limma written 9.6 years ago by Maxim170 • updated 9.6 years ago by James W. MacDonald51k
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stuck with affy/limma
... Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the geno ...
clustering affy limma written 9.6 years ago by Maxim170
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Problems with Affylimma and AffylmGUI
... Hi, I'm using AffylmGUI to analyze a few.cel files downloaded from GEO. This used to work nicely in former times but now I have problems with a couple of .cel files based on the mouse 430 2.0 array. I installed the the corresponding .db and .cdf files. But AffylmGUI does not link the probesets to ...
cdf affylmgui written 9.8 years ago by Maxim170

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Popular Question 5.6 years ago, created a question with more than 1,000 views. For Gviz: axes related parameters

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