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  • Problem:EDAseq R package

    when I use EDAseq R package to deal with the counts in RNASEQ.it is always have problem.

    Error information as followed:
    > geneLevelData=read.table("htseqcount.txt",sep="\t",header=T,check.names=F)
    > head(geneLevelData)
    gene_id s1 s2 s3 s4
    1 0610005C13Rik 3 5 6 11
    2 0610007P14Rik 33 47 10 4
    3 0610009B22Rik 31 50 6 8
    4 0610009L18Rik 1 3 7 3
    5 0610009O20Rik 42 67 33 20
    6 0610010B08Rik 1 3 16 7
    > rownames(geneLevelData)=geneLevelData[,1]
    > geneLevelData=geneLevelData[,2:ncol(geneLevelData)]
    > head(geneLevelData)
    s1 s2 s3 s4
    0610005C13Rik 3 5 6 11
    0610007P14Rik 33 47 10 4
    0610009B22Rik 31 50 6 8
    0610009L18Rik 1 3 7 3
    0610009O20Rik 42 67 33 20
    0610010B08Rik 1 3 16 7
    > yeast=read.table("LengthAndGC.txt",sep="\t",header=T)
    > head(yeast)
    Gene length gc
    1 Itm2a 1632 0.4264706
    2 Sergef 1460 0.5589041
    3 Fam109a 2335 0.6197002
    4 Dhx9 4613 0.4454802
    5 Fam71e2 2686 0.5193596
    6 Ssu72 1451 0.5348036
    > rownames(yeast)=yeast[,1]
    > colnames(yeast)[2:3]=c("length","gc")
    > colnames(yeast)[2:3]
    [1] "length" "gc"
    > yeastGC=data.frame(yeast[,3])
    > rownames(yeastGC)=rownames(yeast)
    > colnames(yeastGC)="gc"
    > head(yeastGC)
    gc
    Itm2a 0.4264706
    Sergef 0.5589041
    Fam109a 0.6197002
    Dhx9 0.4454802
    Fam71e2 0.5193596
    Ssu72 0.5348036
    > yeastLength=data.frame(yeast[,2])
    > rownames(yeastLength)=rownames(yeast)
    > colnames(yeastLength)="length"
    > head(yeastLength)
    length
    Itm2a 1632
    Sergef 1460
    Fam109a 2335
    Dhx9 4613
    Fam71e2 2686
    Ssu72 1451
    > filter <- apply(geneLevelData,1,function(x) mean(x)>3)
    > table(filter)
    filter
    FALSE TRUE
    395 4604
    > common <- intersect(rownames(yeastGC),rownames(geneLevelData[filter,]))
    > length(common)
    [1] 4604
    > feature=yeast[,2:3]
    > head(feature)
    length gc
    Itm2a 1632 0.4264706
    Sergef 1460 0.5589041
    Fam109a 2335 0.6197002
    Dhx9 4613 0.4454802
    Fam71e2 2686 0.5193596
    Ssu72 1451 0.5348036
    > library(EDASeq)
    Loading required package: Biobase
    Loading required package: BiocGenerics
    Loading required package: parallel

    Attaching package: 'BiocGenerics'

    The following objects are masked from 'packagearallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

    The following object is masked from 'package:stats':

    xtabs

    The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
    lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unlist

    Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

    Loading required package: ShortRead
    Loading required package: IRanges
    Loading required package: GenomicRanges
    Loading required package: XVector
    Loading required package: Biostrings
    Loading required package: lattice
    Loading required package: Rsamtools
    > data <- newSeqExpressionSet(exprs=as.matrix(geneLevelData[common,]),featureData=feature[common,],phenoData=data.frame(conditions=colnames(geneLevelData),row.names=colnames(geneLevelData),check.names=F))
    Error in assayDataNew(counts = counts, normalizedCounts = normalizedCounts, :
    argument "counts" is missing, with no default
    > length(common)
    [1] 4604
    > newlwb=length(common)
    > newlen=length(common)
    > head(common)
    [1] "Bcl7a" "Bnip3l" "Capzb" "Cachd1" "B9d2" "Ap5s1"
    > data <- newSeqExpressionSet(exprs=as.matrix(geneLevelData[newlen,]),featureData=feature[newlen,],phenoData=data.frame(conditions=colnames(geneLevelData),row.names=colnames(geneLevelData),check.names=F))
    Error in assayDataNew(counts = counts, normalizedCounts = normalizedCounts, :
    argument "counts" is missing, with no default

    how could I deal with the problem?

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