User: Matthias Z.

gravatar for Matthias Z.
Matthias Z.20
Reputation:
20
Status:
New User
Location:
University Medical Center of Münster, Germany
Last seen:
3 months, 3 weeks ago
Joined:
2 years, 2 months ago
Email:
m**************@ukmuenster.de

Posts by Matthias Z.

<prev • 13 results • page 1 of 2 • next >
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Answer: A: ggplots gives errors
... Can you please post your sessionInfo() output? Because an improperly attached ggplot2 would be the most obvious reason. In case you copy and pasted above code you might also want to check, whether there is an irrgeular newline between )) +  and geom_point(), which could cause the trouble, too. ...
written 3 months ago by Matthias Z.20
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Answer: A: Building a pseudo-network based on correlations
... To me it is not clear what your specific question is, so I presume, it is how to display data, which you have already generated and not how to calculate which are the two most similar edges to draw connections to. The suitable ggplot2 geoms to plot connections are  geom_segment() or geom_curve() de ...
written 13 months ago by Matthias Z.20
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Answer: A: ggbio tracks() function handling x axis in the wrong way
... Hello Oswaldo, Indeed, the tracks() function doesn't do any scaling on the provided tracks. As the manual states: "you can use this function to bind any tracks with the same defination [sic] of x axis, for example, sets of time series plots you made." In ordner to scale your tracks consistently, y ...
written 14 months ago by Matthias Z.20
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Comment: C: GSEA-like enrichment score calculation
... Hello Phillip, Thanks for your anwer. I will go with Gordons suggestion here, but I am sure your suggested tests will be of use for future problems. Best regards Matthias ...
written 17 months ago by Matthias Z.20
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Comment: C: GSEA-like enrichment score calculation
... Hello Gordon, Thanks a lot for your answer, this indeed looks tremendously helpful. It seems I was trying to reinvent the wheel here. I will probably be able to use the barcodeplot right away for my project or can at least dissect the function. Anyway this should clearly solve my problems. Best r ...
written 17 months ago by Matthias Z.20
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Comment: C: GSEA-like enrichment score calculation
... Hello Simon, Thanks a lot for your detailed and educational explanation and of course the link to the helpful paper with the formula I was looking for. Luckily the whole significance testing and comparison of various sets is not relevant for my project at the moment, but good to know anyway. Best ...
written 17 months ago by Matthias Z.20
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GSEA-like enrichment score calculation
... Hello everybody, I would like to calculate and plot the enrichment score of a selection from a ranked list, as many readers are familar with the gene set enrichment plots produced by the Broad Institute's GSEA implementation. While the basic principle is clear to me, I failed to understand how the ...
gseabase gsea enrichment analysis written 17 months ago by Matthias Z.20 • updated 17 months ago by Gordon Smyth32k
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Comment: C: fRMA: Applying mouse4302frmavecs on HT_MG-430_PM Arrays
... Hello Matt, Thanks a lot for your help. Your convertPlatform function was exactly, what I was looking for and solved my technical problems. In the meantime I realized, that you also included it as part of frmatools package - sorry for bothering you with that issue. Frankly speaking, the difference ...
written 22 months ago by Matthias Z.20
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Answer: A: fRMA: Applying mouse4302frmavecs on HT_MG-430_PM Arrays
... Hello Matt, Thanks a lot for your answer. Sadly our dataset is very small (two conditions and four biological replicates each), so the creation of a real frma vector package is probably out of the question - at least without third-party data from public repositories.  So I would like to accept you ...
written 22 months ago by Matthias Z.20
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fRMA: Applying mouse4302frmavecs on HT_MG-430_PM Arrays
... Hello everybody, I was wondering, if it is possible/advised to use the fRMA algorithm to also analyse HT_MG-430_PM arrays. The Affymetrix website states that: "The GeneChip HT MG-430 PM Array Plate enables high-throughput expression profiling of 16, 24, or 96 samples at a time using the same indus ...
microarray frma affiymetrix written 22 months ago by Matthias Z.20

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