User: IOM

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IOM20
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Location:
Birmingham
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2 years, 9 months ago
Joined:
4 years, 8 months ago
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i*************************@bwnft.nhs.uk

Posts by IOM

<prev • 18 results • page 2 of 2 • next >
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How to create a data frame with overlapping segments from CNV oncoscan arrays?
... Hi,   Thanks for reading. Any help/ advice on this issue would be much appreciated. Also, if my approach does not make any sense. I have got all CNV calls/segments in .txt (one for every sample) with following structure: For SAMPLE 1 it would be: Chromosome    Start    End    Value chr1    75419 ...
R data frame oncoscan cnvs overlapping segments written 3.2 years ago by IOM20
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genotype function from crlmm package creates next error "Error in quantile.default(M, c(1, 5)/6, names = FALSE) : missing values and NaN's not allowed if 'na.rm' is FALSE"
... Dear all, Thanks for reading. I know that this issue has been discussed many times, but I am not able to find the right solution to it. I have read other posts and the vignette, I have changed the .CEL files number (10. CEL, 50. CEL, >100.CEL) and the same error keeps popping up. I guess that sp ...
crlmm software error genotype function written 3.8 years ago by IOM20
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Comment: C: Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus
... Hi James, What I would to do is the hierarchical clustering and heatmaps, but without anything I can export from Nexus, I can not do it. That is why I wanted to start from the CEL files, not in order to get the CNV ( as I already have that from NEXUS) but for  getting a file with all the samples an ...
written 3.8 years ago by IOM20
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Answer: A: Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus
... Hi James, Thanks for your reply. I already have spoken with a person from Affy, and has said that there is no possible way of exporting anything from Nexus, the analysis has to start from the CEL files. Do you know any tutorial (apart from crlmm) where I can learn how to perform a hierarchical clus ...
written 3.8 years ago by IOM20
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Answer: A: Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus
... Hi James, Thanks for your reply. I already have spoken with a person from Affy, and has said that there is no possible way of exporting anything from Nexus, the analysis has to start from the CEL files. Do you know any tutorial (apart from crlmm) where I can learn how to perform a hierarchical clus ...
written 3.8 years ago by IOM20
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Is there any way of exporting CNV data from Affymetrix SNP 6.0 arrays from Nexus Software for OncoScan?
... Hi everyone, Thanks for reading. I am doing some work with Affymetrix SNP 6.0 arrays using NExus for OncoScan software. I would like to export the data in order to do some hierarchical clustering, heatmaps, correlation matrices, etc, but the only format I can get is a BED format (.BGR) , and it doe ...
cnv nexus for oncoscan affymetrix 6.0 .bgr written 3.8 years ago by IOM20
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Answer: A: Analysing microarray data in BioConductor-The Knowledgeblog
... Thanks Steve, I will do what you say. Cheers IOM ...
written 4.7 years ago by IOM20
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Analysing microarray data in BioConductor-The Knowledgeblog
... Dear all, Thanks for reading.  I have tried to follow this tutorial http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/ however, when I arrive to the point of annotating the results with associated gene symbols I get this error > gene.symbols <- get ...
microarray hgu133plus2 getsymbol error in unlist written 4.7 years ago by IOM20

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