User: carlos.ruiz

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Posts by carlos.ruiz

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Error when subsetting a RaggedExperiment by GenomicRanges
... Hi, I am currently working with RaggedExperiment. I am interested in selecting only the regions of RaggedExperiment that are included in a GenomicRanges. Despite this functionality is included in the vignette and the manual, I have not been able to apply it to my dataset. It does not work with a to ...
genomicranges raggedexperiment written 20 months ago by carlos.ruiz0 • updated 20 months ago by Marcel Ramos ♦♦ 410
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Comment: C: Error invalid class "SummarizedExperiment" when using library("MultiDataSet")
... Hi Sander, I am not able to reproduce your error with the info that you gave me. Could you post the traceback and sessionInfo? Bests, Carlos ...
written 23 months ago by carlos.ruiz0
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nPCs in minfi's Functional Normalization
... Hi, We are doing the QC and normalization of methylation data using minfi. We have decided to apply Functional normalization to get the beta values. We run the function with the default values (nPCs = 2) and, when we plot a PCA of the resulting beta values, we appreciate that they are still associa ...
normalization minfi methylation written 2.7 years ago by carlos.ruiz0
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Error when computing ld with snpStats in big samples
... Hi, I want to compute the linkage disequilibrium between the SNPs of some predifined regions of the genome of around Mb using snpStats. I have downloaded 1000 Genomes VCF files but I am experiencing some errors. I start with a list of target genomic regions in a GRanges. I have created some functi ...
snpstats software error `ld written 3.2 years ago by carlos.ruiz0
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Extract methylation data from a FirehoseData
... Dear all, I am using RTCGAtoolbox package to download data from TCGA. Rigth now, I have a FirehoseData object with all the data available and I want to extract the methylation. If I use getData function:    getData(TCGA, "Methylation") Error in .getListData(object@Methylation, platform) : Please ...
rtcgatoolbox written 3.8 years ago by carlos.ruiz0 • updated 3.8 years ago by samur0

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