User: Juan Fernández Tajes

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Posts by Juan Fernández Tajes

<prev • 18 results • page 1 of 2 • next >
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remove evidence Codes
... Dear List, I have a list of gene.symbol, that looks like that >head(mylist) $cluster.1 [1] "HSP90AB1" "INMT" "CKB" "NR2E1" "ME3" "FAM162A" "KIRREL2" $cluster.2 [1] "ENSG00000212860" "TRADD" "C1QBP" "KIAA1967" "ENSG00000137379" "MAP3K3" "TNFRSF1B" ...
go written 5.7 years ago by Juan Fernández Tajes190 • updated 5.7 years ago by Vincent J. Carey, Jr.6.3k
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Answer: A: methyAnalysis error
... Dear list and Pan, I¹m still having some problems with the methyAnalysis package, after update some functions thanks to Pan I¹m still experiencing some problems with certain functions, for example I am not able to plot the heatmap with >heatmapByChromosome(methyGenoSet, gene='55342', genomicFea ...
written 5.8 years ago by Juan Fernández Tajes190
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methyAnalysis error
... Dear list I¹m trying to convert a MethyLumi object into a GenoSet object, but when I try the following command I got an error: > methyGenoSet <- MethyLumiM2GenoSet(filt, lib="IlluminaHumanMethylation27k.db") Error in `rownames<-`(`*tmp*`, value = c("cg00000292", "cg00002426", "cg00003994" ...
go convert methylumi genoset written 5.8 years ago by Juan Fernández Tajes190
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xps problem with root files
... Dear list, I´ve already analysed microarray data from Hugene11 st with oligo package. However I would like to use xps package as well because I want to compare results from Hugene 1.0 and Hugene 1.1 and I think xps package is the right one. I have created the root scheme following the script propo ...
microarray xps written 6.9 years ago by Juan Fernández Tajes190 • updated 6.9 years ago by cstrato3.9k
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Comment: C: Analyzing expression Affymetrix Hugene1.0.st array
... Dear Jim and Steve, Many thanks for your answers and for your tips. I´ve learn a lot and I´ll try to tell all this information to my supervisor. Many thanks again Juan --------------------------------------------------------------- Juan Fernandez Tajes, ph. D Grupo XENOMAR Departamento de Biol ...
written 6.9 years ago by Juan Fernández Tajes190
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Comment: C: Analyzing expression Affymetrix Hugene1.0.st array
... Benilton , Many thanks for your response, the problem is that I´m trying to get levels of gene expression (but whithout comparing different samples) from arrays and I think it is not a good approach. I´m already posted to Bioconductor list the question about possibility to obtain that kind of inf ...
written 6.9 years ago by Juan Fernández Tajes190
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Comment: C: Analyzing expression Affymetrix Hugene1.0.st array
... Dear James, Many thanks for your quick and easy understable question. I would like to ask you if you could recommend me a method to determine which point could be considered as level for distinguishing expression values from noise? Juan ------------------------------------------------------------ ...
written 6.9 years ago by Juan Fernández Tajes190
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Analyzing expression Affymetrix Hugene1.0.st array
... Dear List, I´m working with expression data obtained from Affymetrix HuGene 1.0 st array. I´m interested in knowing how many genes are expressed in chromosome 16. Surprisingly, all the genes included (808) in the array and mapped to chromosome have expression values (from 2.01 to 12.4), can I con ...
written 6.9 years ago by Juan Fernández Tajes190 • updated 6.9 years ago by James W. MacDonald50k
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Comment: C: paCalls oligo package
... Hi Jim, Sorry for bothering you, but I need to clarify my code because I think I´ve misunderstood something, here is the code that I´m using: > dat <- affyGeneFS > sampleNames(dat) <- sub("\\.CEL$", "", sampleNames(myAB)) > metadata_array <- read.delim(file="metadata_array_olig ...
written 6.9 years ago by Juan Fernández Tajes190
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Comment: C: paCalls oligo package
... Hi James, Many thanks for your answer, for instance, I want to check if the probeset intensities for a given transcript are significantly brighter than background probesets, but I wasn´t able to explain it properly. I have another question regarding your explanation: > Also note that it appear ...
written 6.9 years ago by Juan Fernández Tajes190

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