User: sofia.figueiredo

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2 years, 7 months ago
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Posts by sofia.figueiredo

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Using Pathview with gene.idtype = "SYMBOL"
... Dear Bioconductor community, I want to map my FC data to a Pathway using pathview like this: > pv.out <- pathview(gene.data = Nn.matrix[, 1], gene.idtype = "SYMBOL", pathway.id = "04110", species = "hsa", out.suffix = "Nn", kegg.native = TRUE) However, I get the following error: Error in ...
pathview symbol written 2.7 years ago by sofia.figueiredo10
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Comment: C: Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster
... Many thanks for your clarifications. I normalized my data again, adding the option target="core" to the rma function and did the annotations with hugene20sttranscriptcluster.db. Everything is working fine :) Sofia ...
written 2.8 years ago by sofia.figueiredo10
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Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster.db hugene20sthsentrezg or hugene20stprobeset
... Dear Bioconductor community, I am working with Human Gene 2.0 ST Array. At the annotation process, I have doubts which .db library to use: - hugene20sttranscriptcluster.db - hugene20sthsentrezg.db or - hugene20stprobeset.db? Can you please indicate what are the differences between these three a ...
hugene20sttranscriptcluster.db affymetrix microarrays written 2.8 years ago by sofia.figueiredo10 • updated 2.8 years ago by James W. MacDonald49k
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Answer: A: arrayQualityMetrics does not complete successfully
... Dear Bioconductor community, I am having exactly the same problem. > celfiles <- rma (read.celfiles (list) ) > arrayQualityMetrics (expressionset=celfiles, outdir="Report for celfile RMA", force=TRUE) The report will be written into directory 'Report for celfile RMA'. Error in file.info ...
written 2.8 years ago by sofia.figueiredo10

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