10 GEO探针ID转换成gene symbol

在r软件中,

> mydata<-read.table("C:/Users/a/Desktop/immunoscore/GSE29272_series_matrix.txt",sep="\t",header=TRUE)

> library(AnnotationDbi)

Loading required package: stats4

Loading required package: BiocGenerics

Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,

    clusterExport, clusterMap, parApply, parCapply, parLapply,

    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,

    colnames, colSums, dirname, do.call, duplicated, eval, evalq,

    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,

    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,

    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans,

    rownames, rowSums, sapply, setdiff, sort, table, tapply, union,

    unique, unsplit, which, which.max, which.min

Loading required package: Biobase

Welcome to Bioconductor

    Vignettes contain introductory material; view with

    'browseVignettes()'. To cite Bioconductor, see

    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

> library(hgu133a.db)

Loading required package: org.Hs.eg.db

> k <- mydata$Scan.REF

> out<-select(hgu133a.db,keys=k,cols=c('SYMBOL','GENENAME'),keytype='PROBEID')

Error in .select(x, keys, columns, keytype, jointype = "probes.probe_id",  : 

  argument "columns" is missing, with no default

转换的最后一步语句报错:

Error in .select(x, keys, columns, keytype, jointype = "probes.probe_id",  : 

  argument "columns" is missing, with no default
请问这个怎么改

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1 个回答

祝让飞 - 生物信息工程师

out<-select(hgu133a.db,keys=k,cols=c('SYMBOL','GENENAME'),keytype='PROBEID')

换成:

out<-select(hgu133a.db,keys=k,columns=c('SYMBOL','GENENAME'),keytype='PROBEID')

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  • gerychance 提出于 2018-08-22 14:21

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