User: thrabe

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thrabe0
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Posts by thrabe

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Comment: C: coefmap plot - label colors
... Ok, I'll divert my questions to other resources then. Thought to be able to reach experienced users here.   ...
written 3.9 years ago by thrabe0
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coefmap plot - label colors
... I am using the coefmap plot to display NMF based classification of my data. When I add the sample labels to the plot, it will highlight a colored bar under the classification tree to indicate where data came from. The default colors are difficult to distinguish in presentations (blue, dark purple, l ...
affy nmf coefmap written 3.9 years ago by thrabe0 • updated 3.9 years ago by James W. MacDonald51k
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Coefmap plot without the sorting
... The sample data that I have is labeled into few classes. When I run the coefmap command on the ExpressionMix / blood sample, the samples are shuffled by classification. Thats great of course. But I would like to have the same plot but with the samples unshuffled (without the hirarchical clustering s ...
cellmix coefmap written 3.9 years ago by thrabe0
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Answer: A: Access MarkerList attribute
... That darn package has a built in function "geneValues" to read the attribute. Please excuse my french, but the way the library is structured and documented sucks. ...
written 3.9 years ago by thrabe0
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Access MarkerList attribute
... How can I access the geneValues attribute of a MarkerList object from the CellMix package? When I just type the name of the object, I get this:   >sml Types: Th act, Tc act, ..., neutro (total: 10) Mode: numeric setName: Abbas geneIds: 234408_PM_at, 243110_PM_x_at, ..., 229967_PM_at (total: ...
cellmix written 3.9 years ago by thrabe0
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basismarkermap scaling fails for large data
... Hi there, I have trouble with the basismarkermap plot. The ExpressionMix I use is contains 115 samples, and when I plot it with HaemAtlas markers mapped onto Affymatrix IDs the final plot is extremely detoriated, the matrix is half truncated at the right edge for instance. The cause for this behavio ...
cellmix written 3.9 years ago by thrabe0
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Comment: C: Get ID Mapping right
... The thing that freaks me out about the makeDBPackage function is that is does not return anything and no verbose. Is there a way to enable feedback? I do not see anything happen and the function finishes immediately. I am not sure if he finds the files or not. Absolute vs relative paths and so forth ...
written 3.9 years ago by thrabe0
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Comment: C: Get ID Mapping right
... Thank you James. I'll have a look. I'm new to this whole field. Sorry for bugging you with all those questions. ...
written 3.9 years ago by thrabe0
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Comment: C: Get ID Mapping right
... Thanks. I tried that, didnt get too far. See my at under the other thread. ...
written 3.9 years ago by thrabe0
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Comment: C: AnnotationDbi packages missing in current release
... Hi Isaac, I tried your code, but it fails for me. Sorry to bug you, but I am new to all this. I downloaded the CVS of hthgu133, but am getting nowhere with my commands. Can you please help? library(AnnotationForge) #library(org.Rn.eg.db) #library(rat.db0) makeDBPackage("HT_HG_U133_Plus_PM", affy = ...
written 3.9 years ago by thrabe0

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Popular Question 3.9 years ago, created a question with more than 1,000 views. For CEL to Cibersort mix files, fails find Affymatrix specs

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