User: anthonycolombo60

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Posts by anthonycolombo60

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Answer: A: R CMD check S3 generic/method consistency WARNING
... I was able to remove this warning by greatly reducing my Depends section to only 1 really needed package.  once I reduced my depends, this warning disappeared. ...
written 15 months ago by anthonycolombo600
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R CMD check S3 generic/method consistency WARNING
... Hello to all.  I am in the process of writing a package and have 4 warnings.  2 warnings have to deal with S3 set generic/method consistency and setReplacement methods.  the other 2 are Rd \usage warnings. this post is about the 2 warnings about the generics and replacement methods:   * checking ...
cmd check warnings s3 written 15 months ago by anthonycolombo600 • updated 15 months ago by Gordon Smyth32k
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RUVSeq empirical negative controls? how many to take to find the span set
... Hi. so I am using RUVg(eset, k=1,...)   determining the in-silico negative controls by gene or transcript that has a p.value greater than 0.55 with the FDR procedure Benj-Hoch (many many highly insignificant entries came up).   my question is I am not sure how many to include as insignificant entr ...
ruvseq ruv ruvg ruvnormalize written 16 months ago by anthonycolombo600
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Answer: A: RUVSeq DE analysis for data with replicate samples and 4 conditions
... Hi.  so for contrasts with the RUVSeq factors, do you set them to zero?  in this example above lrt <- glmLRT(fit, contrast=c(0, -1, 1, 0, 0))  the fifth column is the W_1 from RUVSeq, but does this take into account the unwanted variance factor?  it appears the fit is contrasting  Cov_3/Cov_2  ...
written 17 months ago by anthonycolombo600
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Comment: C: GEO MicroArray Download, Annotation, and Main Probe Filtering
... I solved it using this   library(affy) library(oligo) celFiles<- list.celfiles(getwd(),listGzipped=TRUE) affyRaw<-read.celfiles(celFiles) #library(pd.hg.u133a.2)  eset<-rma(affyRaw) library(hgu133a2.db) Annot<-data.frame(ACCNUM=sapply(contents(hgu133a2ACCNUM), paste, collapse=", "), S ...
written 22 months ago by anthonycolombo600
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Comment: C: GEO MicroArray Download, Annotation, and Main Probe Filtering
... If I use the select() method the symbols are NA  test<-select(hgu133a2.db,affyids,"SYMBOL","PROBEID") head(test)    PROBEID SYMBOL 1 10000_at   <NA> 2 10001_at   <NA> 3 10002_at   <NA> 4 10003_at   <NA> 5 10004_at   <NA> 6 10005_at   <NA> > the amount of ...
written 22 months ago by anthonycolombo600
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Answer: A: GEO MicroArray Download, Annotation, and Main Probe Filtering
... okay thank you   I was able to solve using the oligo package as well.       celFiles<- list.celfiles(getwd(),listGzipped=TRUE) affyRaw<-read.celfiles(celFiles) library(pd.hg.u133a.2)  eset<-rma(affyRaw) Annot<-data.frame(ACCNUM=sapply(contents(hgu133a2ACCNUM), paste, collapse=", ") ...
written 22 months ago by anthonycolombo600
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GEO MicroArray Download, Annotation, and Main Probe Filtering
... Hi.  This is a similiar issue reported here  : https://support.bioconductor.org/p/60577/ So I'm annotating a microarray .CEL data pulled from GEO by an accession number using GEOquery, and am unable to annotate the resultant expression set using BiomaRt (using the respective hg_u133a_2.db).  The e ...
microarray affy biomart written 22 months ago by anthonycolombo600
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GitHub Continuous Integration, unit-tests, vignettes: R Packaging
... Hi.   I'm writing a software package on github, and wishing to prepare for submission to Bioconductor channels that synchronizes TRAVIS continuous integration.  Currently I'm setting up the TRAVIS environment dependencies, and soon will have to write unit-tests for the package commits.     I wis ...
developers github vignette test written 23 months ago by anthonycolombo600 • updated 23 months ago by Dan Tenenbaum ♦♦ 8.2k
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Using Ensmbl rel 80, when rel 79 is supported by BioConductor
... Hi.   First thank you for any advice.   I am using external software that processes Ensmbl_GRCh38.rel80 for homo sapiens for data processing.   When I bring the data into R, the annotation that is available for H.Sapiens is rel79.   This is a discrepancy that I wish to clear up.   Should I ...
ensembl written 2.3 years ago by anthonycolombo600 • updated 2.3 years ago by Johannes Rainer1.0k

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