User: John Lande

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John Lande280
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Posts by John Lande

<prev • 28 results • page 1 of 3 • next >
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Answer: A: pam implementation
... thank you both for the answer. the point is that pamr lacks of a specific vignette as other bioc packages so I was wondering if it was discontinued somehow. is there around a tutorial that explains pipelines of analysis and functions? bests On Fri, Nov 2, 2012 at 7:42 PM, Wolfgang Huber wrote: ...
written 6.5 years ago by John Lande280
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Answer: A: pam implementation
... dear all, what is the best implementation in R or Bioconductor of the PAM algorithm probosed by Tibshirani et colleague? best reguards [[alternative HTML version deleted]] ...
written 6.6 years ago by John Lande280
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pam implementation
... dear all, what is the best implementation in R or Bioconductor of the PAM algorithm probosed by Tibshirani et colleague? best reguards [[alternative HTML version deleted]] ...
written 6.6 years ago by John Lande280
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Answer: A: AgiMicroRna with single channel Agilent Array
... Indeed you are right, I was confused by the fact that the package didn accpted my data. however I found that the Agilent Feature Extraction is different from the one used in the package. the software is version 10.7.3.1. do you think this could be the problem? I found that I miss some columns in t ...
written 7.8 years ago by John Lande280
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AgiMicroRna with single channel Agilent Array
... dear Bioc, I have a simple problem. I just got some Agilent single channel data for miRNA to analyse. I check in BioC repository and found the package AgiMicroRna that seems fits my need, however it seems to me that it can only handle 2 channel experiment. do you know any way to properly handle t ...
agimicrorna written 7.9 years ago by John Lande280
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biomaRt still in trouble
... dear BioC I still have problem regarding biomart if I run > ensembl <- useMart("ensembl") > ensembl_human <- useDataset("hsapiens_gene_ensembl", mart=ensembl) > EnsTS <- getGene(id = as.vector(TS[,1]), type="entrezgene", mart=ensembl_human) Error in getBM(attributes = attrib, fi ...
written 8.2 years ago by John Lande280 • updated 8.2 years ago by Steffen Durinck540
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AnnotationDbi
... dear All, I am trying to build an annotation package with annotationDbi. I followed the instruction to build the package, with this script: #### library(AnnotationDbi) Illumina_8v <- 'ilmn_cust_raw.txt' myMeta = c("DBSCHEMA"="illumina", "ORGANISM"="Homo sapiens", "SPECIES"="Human", "MANUFACTURE ...
annotation affy annotationdbi written 9.3 years ago by John Lande280
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lambda and other questions related to siggenes
... dear all, recently I tried old scripts running siggenes function. to have reproducibility with sam in excel I used the option lambda=0.5. now it seems that with siggenes 1.20.0 this option is not available. did it simply changed the name, or it was removed? furthermore if I run the summary I am n ...
go hgu133a siggenes written 9.5 years ago by John Lande280
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AnnBuilder?
... dear All, I used to analyse old custom chips long time ago, and to generate annotation i took advantage of AnnBuilder. I just found that this package is discontinued in current Bioconductor release. is there any package that generate annotation for custom chips in place for AnnBuilder? -- John ...
annotation annbuilder written 9.5 years ago by John Lande280 • updated 9.5 years ago by Heidi Dvinge2.0k
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clustalW
... dear all, is there a an implementation of clustalw in bioconductor? -- John [[alternative HTML version deleted]] ...
written 9.5 years ago by John Lande280 • updated 9.5 years ago by Michael Lawrence620

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