User: Renaud Gaujoux

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Posts by Renaud Gaujoux

<prev • 16 results • page 1 of 2 • next >
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Answer: A: CellMix package use with own data matrix
... Hi Maria, note that you do not need to use an ExpressionSet object. Plain matrix objects should work as well, as long as the rownames match: x <- as.matrix(read.table('mixed_ data.tsv', sep = "\t")) y <- as.matrix(read.table('celltype_data.tsv', sep = "\t")) res <- gedProportions(x, y, re ...
written 5.2 years ago by Renaud Gaujoux170
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CellMix package use with own data matrix
... Hi, you should be able to run any method on a simple matrix object like your own data. Please send me a sample code that breaks if you think there is a bug. However, I would suggest you to still wrap your data into an ExpressionSet objects, if you have phenotypic covariates data as well. They just ...
written 5.3 years ago by Renaud Gaujoux170
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GEOquery: incomplete feature data from GPL soft file
... Hi, I am getting incorrect feature annotation data when loading a dataset from GPL4133. The feature data looks like this: head(fData(eset)[, 1:2]) ID COL 12 12 266 NA NA.1 15 15 266 16 16 266 NA.2 This possibly also results in having less features in the final expre ...
annotation geoquery written 6.1 years ago by Renaud Gaujoux170
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Comment: C: On extending class ExpressionSet
... I get your point with the multiple inheritance example, but I did not mean to give a general work around for all inheritance situation, but rather for the specific case of the initialize method of class ExpressionSet. I understand that touching class ExpressionSet is a very sensitive matter given it ...
written 8.6 years ago by Renaud Gaujoux170
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Comment: C: On extending class ExpressionSet
... Hi Morgan, thank you very much for the explanation on the initialize method for the class ExpressionSet. I always found the S4 initialization mechanism a bit difficult to handle in the case of inheritance. It often requires to manually pass slots to the parent class, which should be automatic: each ...
written 8.6 years ago by Renaud Gaujoux170
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On extending class ExpressionSet
... Hi, I am trying to extend class ExpressionSet in a very simple way to add an extra slot. Now suppose I have a valid ExpressionSet object, I want to create an object of class 'A' as follows (this always worked with other S4 classes I defined): library(Biobase) setClass('A', representation(extraslot ...
written 8.6 years ago by Renaud Gaujoux170 • updated 8.6 years ago by Martin Morgan ♦♦ 23k
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CMA package: variable selection with limma
... Hi, I used the CMA package (v1.0.0) to evaluate the performance of a kNN classification after a feature selection step using limma, including the whole procedure in the cross-validation. Before finding the CMA package I had implemented myself the same procedure (cross-validation ...
microarray classification regression limma cma written 10.4 years ago by Renaud Gaujoux170
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SimpeAffy: how to get/generate qcdef file?
... Great thanks. All right, I tried it but I got these error messages: Again unable to find the file even if I ran a setQCEnvironment giving the clean name and the path to the file. > AffyQA(parameters = c("part"), raw = eset) [1] "Retrieving grouping parameters" Error in setQCEnvironment(genome) ...
cdf probe affy simpleaffy written 10.5 years ago by Renaud Gaujoux170 • updated 10.5 years ago by claire wilson30
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Answer: A: SimpeAffy: how to get/generate qcdef file?
... Hi, I actually read the vignette but how do you get all the information needed to create the file? I guess the qcdef file showed in vignette will not work as it is for a sugar cane array (even changing the header name to sugarcanecdf). Do I have to look by eye at the cdf file and extract the info? ...
written 10.5 years ago by Renaud Gaujoux170
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SimpeAffy: how to get/generate qcdef file?
... Hi list, how can one generate the qcdef file required by SimpleAffy in the case of a sugarcane Affymetrix array. I installed and loaded the sugarcanecdf package. Since it is in the Bioconductor repository I thought the qcdef file would come together. Is there a function that generate the qcdef file ...
cdf simpleaffy written 10.5 years ago by Renaud Gaujoux170

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