User: Peter Kupfer

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Peter Kupfer70
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Posts by Peter Kupfer

<prev • 7 results • page 1 of 1 • next >
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ggplot2 and the legend
... Dear all, i try to plot with ggplot2. Therefor I have an matrix with 3 colums. With cbind I add an additional column called "col". I need this column "col" because in a later step and want to specify here some plot details which I will get from another analysis If I want to plot with this code, I ha ...
written 6.6 years ago by Peter Kupfer70 • updated 6.6 years ago by Paul Theodor Pyl80
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Comment: C: PAMR- Package: Workflow and/or other methods
... Thanks Sean, but i guess: The included methods are not so different to methods in the e1071-package. I guess: For thousands of genes it is a little bit difficult or? Maybe I have to choose an other method. You suggest one? Thanks Peter Am 19.11.2012 um 16:29 schrieb Sean Davis : > > > &g ...
written 6.6 years ago by Peter Kupfer70
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PAMR- Package: Workflow and/or other methods
... Dear all, i searched for a classification method for microarrays with 3 groups. Therefore I found the package "PAMR" which works out for the example data and with the tutorial ( http://www- stat.stanford.edu/~tibs/PAM/Rdist/doc/readme.html ) Well, i tried it with my data and the output is not so goo ...
classification written 6.6 years ago by Peter Kupfer70 • updated 6.6 years ago by Sean Davis21k
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Packages for differentially expressed genes
... Dear all, first time for my to work with steady state data. Two groups and 30 arrays (hgu133a- arrays) in total. In the past I worked with time course and/or limma to detect differentially expressed genes. Are there any packages which you would recommend for the detection of differentially expressed ...
limma written 6.6 years ago by Peter Kupfer70 • updated 6.6 years ago by Gordon Smyth37k
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Comment: C: ComBat: Comparison of data
... Thanks Evan! So I did the right comparison methods in the past. Further question: Is there any possibility to get the code which you used to plot the shrinkage plots as showed in your paper? Thanks and all the best Peter Am 29.10.2012 um 15:39 schrieb "W. Evan Johnson" : > Peter, > > U ...
written 6.7 years ago by Peter Kupfer70
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ComBat: Comparison of data
... Dear all, i deal with the tool ComBat and try to remove underlying batch effects. Therefor I used covariates and recommend in the manual. After correcting the data and want to have a glue, what the tool did. Therefor i am looking for a method for comparing the corrected and the uncorrected data. Is ...
written 6.7 years ago by Peter Kupfer70
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Answer: A: ComBat: Comparison of data
... Dear all, i deal with the tool ComBat and try to remove underlying batch effects. Therefor I used covariates and recommend in the manual. After correcting the data and want to have a glue, what the tool did. Therefor i am looking for a method for comparing the corrected and the uncorrected data. Is ...
written 6.7 years ago by Peter Kupfer70

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