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User: Javier Pérez Florido

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Posts by Javier Pérez Florido

<prev • 91 results • page 1 of 10 • next >
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enrichGO (clusterProfiler) produces different results
... I'm using enrichGO function from clusterProfiler package to run a functional enrichment analysis using a set of annotated peaks from a chip-seq experiment (the input is the list of genes obtained by the annotation of peaks, human). Using the same input data, I'm getting different results from enric ...
chipseq clusterprofiler go enrichment written 11 months ago by Javier Pérez Florido840 • updated 11 months ago by Guangchuang Yu1.1k
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Comment: C: error in sort.int , 'x' must be atomic in affy::boxplot
... Thanks James, What a mistake. affyPLM was loaded in the script in which boxplot worked well for the normalized data. But it was not loaded in the other script where boxplot fails...that was the point: boxplot method from affyPLM was the one working. Thanks again and apologize for this mess. I'm as ...
written 23 months ago by Javier Pérez Florido840
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Comment: C: error in sort.int , 'x' must be atomic in affy::boxplot
... Dear James, Thanks for your quick and useful reply. Yes, you are right: affy does not define a boxplot nor a hist function for an expression set object. However, I've used boxplot and hist with normalized objects before (same type of microarray). In fact, before asking this question, I've tried wit ...
written 23 months ago by Javier Pérez Florido840
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error in sort.int , 'x' must be atomic in affy::boxplot
... Dear list, I'm using affy package for analyzing a dataset (Affymetrix, hgu133plus2). boxplot and hist work fine with raw data. However, after preprocessing with rma, the following error is obtained when using boxplot and hist on normalized data: celfiles.rma <- rma(celfiles) boxplot(celfiles.r ...
hgu133plus2 boxplot oligo package affy package written 23 months ago by Javier Pérez Florido840 • updated 23 months ago by James W. MacDonald49k
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Comment: C: contrast matrix design for a comparison (trend) of drug concentrations
... Thanks Aaron for your reply. What would be the difference if instead of con <- makeContrasts(concLow - control, concMed - concLow, concHigh - concMed, levels=design) we design the following contrasts: con <- makeContrasts(concLow - control, concMed - control, concHigh - control ...
written 2.3 years ago by Javier Pérez Florido840
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contrast matrix design for a comparison (trend) of drug concentrations
... Dear list, I have a microarray experiment with several samples grouped as: control, drug_conc_a, drug_conc_b, drug_conc_c. That is, a control group and then other groups with different concentrations of a drug (same drug): a, b and c Besides the comparisons of the control group with respect to eac ...
limma affymetrix microarrays limma contrast matrix written 2.3 years ago by Javier Pérez Florido840 • updated 2.3 years ago by Aaron Lun22k
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Comment: C: strange pseudo-image plot from MoGene 2.0 array
... Great, thanks! I didn't know the existence of this package (affxparser). Best, Javier   ...
written 2.3 years ago by Javier Pérez Florido840
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strange pseudo-image plot from MoGene 2.0 array
... Dear list, I'm running a microarray analysis from an Affymetrix MoGene 2.0 ST array set. The first obvious step in the analysis is to inspect the quality of the dataset using several metrics (boxplots, histograms, pseudo-images etc). Oligo package provides several utilities for this purpose. I'm a ...
oligo affymetrix mouse gene arrays pseudoimage oligo package written 2.3 years ago by Javier Pérez Florido840 • updated 2.3 years ago by James W. MacDonald49k
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Affymetrix mogene 2.0 annotation data vs 2.1
... Dear list, I was wondering the differences between annotation packages mogene20sttranscriptcluster.db and mogene21sttranscriptcluster.db. I assume that they are both related to MoGene ST 2.0 chip (couldn't find chip 2.1 in affymetrix site), but not sure what's new in mogene2.1 annotation file with r ...
affymetrix mouse gene arrays written 3.4 years ago by Javier Pérez Florido840 • updated 3.4 years ago by Guido Hooiveld2.4k
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Comment: C: get al microRNA target sites for a given gene
... Hi James, Thanks for your reply. What I want is something like this: http://docs.bioinfo.cipf.es/projects/cellbase/wiki/Feature_rest_ws_api Cellbase retrieves all microRNA targets sites for a given gene, for example, for BRCA2 gene: * http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/ ...
written 6.3 years ago by Javier Pérez Florido840

Latest awards to Javier Pérez Florido

Popular Question 11 months ago, created a question with more than 1,000 views. For problems using the latest version of e1071 (svm)
Popular Question 11 months ago, created a question with more than 1,000 views. For svm (e1071) class weighting in a multi-class problem
Popular Question 11 months ago, created a question with more than 1,000 views. For error in sort.int , 'x' must be atomic in affy::boxplot
Popular Question 23 months ago, created a question with more than 1,000 views. For svm (e1071) class weighting in a multi-class problem

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