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design matrix in limma
... Hello BioC forum, I am making a design matrix for gene expression data analysis with the adjustment of Sex variable. The R code I am using is below. I want to make sure if I am doing correctly. Thanks for your review and feedback. > library(limma) > Sample<-factor(pd$Sample_Group, level ...
written 3.2 years ago by Guest User12k • updated 3.2 years ago by Bernd Klaus470
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HGU133Plus2 CDF vs hgu133plus2hsentrezgcdf CDF (30% difference in results)
... Hello, My name is Mahes Muniandy and I am a doctoral student. I have been analysing Affymetrix HGU133Plus2 cel files to determine differential expressions in twin pairs (within pair differences). I have used affy, gcrma, nsfilter and limma to do my analysis. I have run my analysis using the HGU133pl ...
go hgu133plus2 cdf affy limma written 3.2 years ago by Guest User12k • updated 3.2 years ago by Steve Lianoglou12k
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Bioinformatics researching Schizophrenia
... I am an undergraduate student and I have been given a project that involves bioinformatics. My supervisor researches chromosome abnormalities and gene expression and he has been given a list of GWAS generated SNPs, that have been linked to Schizophrenia and it has been assigned to me to generate a l ...
mirna written 3.2 years ago by Guest User12k • updated 3.2 years ago by Valerie Obenchain ♦♦ 6.4k
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Ask help for Rcpp
... Does anyone know how to use regex in Rcpp for Bioconductor package development? Best regards! Bo -- output of sessionInfo(): No -- Sent via the guest posting facility at bioconductor.org. ...
written 3.2 years ago by Guest User12k • updated 3.2 years ago by Martin Morgan ♦♦ 20k
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log2 as input in limma
... Hi all, I have performed batch-normalization on my RNA-Seq data leaving the data as cpm-log2 normalized. How do I use this as input in limma? It usually only take count data. -- output of sessionInfo(): none -- Sent via the guest posting facility at bioconductor.org. ...
written 3.2 years ago by Guest User12k • updated 3.2 years ago by James W. MacDonald45k
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no method for coercing S4 class to a vector
... Dear all, I have a similar problem to this poster here: http://grokbase.com/t/r/bioc-devel/141cegqvpf/no-method-for-coercing- this-s4-class-to-a-vector The error message is: Error in as.vector(x) : no method for coercing this S4 class to a vector In my case, however, I'm using the as.data.fra ...
written 3.2 years ago by Guest User12k • updated 3.2 years ago by Andrzej Oleś670
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Error using Bsmooth.tstat due to NAs
... Dear all, I am trying to use bsseq to analyze WGBS data and identify DMRs following drug treatment. I have a BSseq object consisting of 2 samples (treated and ctrl) that has been smoothed: >smooth An object of type 'BSseq' with 38250590 methylation loci 2 samples has been smoothed with BS ...
coverage bsseq written 3.2 years ago by Guest User12k • updated 2.7 years ago by parker0
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Organism annotation package created with makeOrgPackage doesn't install properly
... I work with the plant Sorghum bicolor and want to make my own organism annotation package. I created package with makeOrgPackage and also tried the example in: http://www.bioconductor.org/packages/release/bio c/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.html They both were created ...
go written 3.2 years ago by Guest User12k • updated 3.2 years ago by James W. MacDonald45k
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barcode support for other platforms
... I am trying to assess whether genes in my samples are over expressed relative to a null mean. I use the barcode function in the R package frma for this purpose. As far as I understand the current Barcode version support only Affymetrix and only three platforms in it : GPL570, GPL96 and GPL1261. I d ...
frma written 3.2 years ago by Guest User12k • updated 3.2 years ago by Matthew McCall760
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Gostats Hypergeometric tests for non model organisms Kegg pathway
... Hello I would like to run an hypergeometric testing on KEGG terms for non- model organism. When it comes to Goterm I always use Gostats where I can enter my "universe" list and then my "target" genes and it works really well. However, when it comes to Kegg pathways, I tried to use go stats again b ...
pathways go organism gostats written 3.2 years ago by Guest User12k

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