Closed patriciaB96 closed 3 years ago
Hi, I tried to reproduce the code with the provided hepatocyte dataset, I followed the protocol as indicated:
library(PhosR) phospho_hepatocyte_raw <- (PXD001792_raw_hepatocyte.txt) del <- which(phospho_hepatocyte_raw[,"Reverse"]=="+" | phospho_hepatocyte_raw [,"Potential.contaminant"]=="+") phospho_hepatocyte_clean <- phospho_hepatocyte_raw[-del,] PXD001792_raw_hepatocyte <- phospho_hepatocyte_clean[,grep("Intensity", colnames(phospho_hepatocyte_clean))] ppe <- PhosR::PhosphoExperiment(assays = list(Quantification = as.matrix(PXD001792_raw_hepatocyte))) GeneSymbol <- toupper(sapply(strsplit(as.character(phospho_hepatocyte_clean [,"Gene.names"]), ";"), function(x){x[1]})) Residue <- as.character(phospho_hepatocyte_clean [,"Amino.acid"]) Site <- as.numeric(phospho_hepatocyte_clean [,"Position"]) Sequence <- sapply(strsplit(as.character(phospho_hepatocyte_clean[,"Sequence.window"]), ";"), function(x){x[1]}) ppe@GeneSymbol <- GeneSymbol ppe@Residue <- Residue ppe@Site <- Site ppe@Sequence <- Sequence ppe <- PhosphoExperiment(assays = list(Quantification = as.matrix(PXD001792_raw_hepatocyte)), Site = Site, GeneSymbol = GeneSymbol, Residue = Residue, Sequence = Sequence) samplename <- strsplit(gsub("^Intensity.", "", colnames(ppe)), "") df <- S4Vectors::DataFrame( cellline = sapply(sample_name, "[[", 1), condition = sapply(sample_name, "[[", 2), replicate = sapply(sample_name, "[[", 3) )
But get the following error here: "Error in FUN(X[[i]], ...) : subscript out of bounds"
Can somebody help me maybe?
Hi, I tried to reproduce the code with the provided hepatocyte dataset, I followed the protocol as indicated:
library(PhosR) phospho_hepatocyte_raw <- (PXD001792_raw_hepatocyte.txt) del <- which(phospho_hepatocyte_raw[,"Reverse"]=="+" | phospho_hepatocyte_raw [,"Potential.contaminant"]=="+") phospho_hepatocyte_clean <- phospho_hepatocyte_raw[-del,] PXD001792_raw_hepatocyte <- phospho_hepatocyte_clean[,grep("Intensity", colnames(phospho_hepatocyte_clean))] ppe <- PhosR::PhosphoExperiment(assays = list(Quantification = as.matrix(PXD001792_raw_hepatocyte))) GeneSymbol <- toupper(sapply(strsplit(as.character(phospho_hepatocyte_clean [,"Gene.names"]), ";"), function(x){x[1]})) Residue <- as.character(phospho_hepatocyte_clean [,"Amino.acid"]) Site <- as.numeric(phospho_hepatocyte_clean [,"Position"]) Sequence <- sapply(strsplit(as.character(phospho_hepatocyte_clean[,"Sequence.window"]), ";"), function(x){x[1]}) ppe@GeneSymbol <- GeneSymbol ppe@Residue <- Residue ppe@Site <- Site ppe@Sequence <- Sequence ppe <- PhosphoExperiment(assays = list(Quantification = as.matrix(PXD001792_raw_hepatocyte)), Site = Site, GeneSymbol = GeneSymbol, Residue = Residue, Sequence = Sequence) samplename <- strsplit(gsub("^Intensity.", "", colnames(ppe)), "") df <- S4Vectors::DataFrame( cellline = sapply(sample_name, "[[", 1), condition = sapply(sample_name, "[[", 2), replicate = sapply(sample_name, "[[", 3) )
But get the following error here: "Error in FUN(X[[i]], ...) : subscript out of bounds"
Can somebody help me maybe?