DEXSeq 分析を実行していますが、DEXSeqDataSetFromSE に到達すると、次のエラーが発生します。このスクリプトを数回使用してうまくいきましたが、今回はさらに 2 つの生物学的複製を追加したところ、このエラーが発生しました。どんな助けにも感謝します。
DEXSeq : DESeqDataSet のエラー (rse、design、ignoreRank = TRUE
library(GenomicRanges)
library(GenomicFeatures)
library(GenomicAlignments)
library(DEXSeq)
#Download the human genome we aligned to hg19
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
hse <- TxDb.Hsapiens.UCSC.hg19.knownGene
#Collapse Gene models into counting bins. The exonicParts object contains a GRanges object with our counting bins. We use it to count the number of read fragments that overlap with the bins by means of the function
exonicParts = exonicParts( hse, linked.to.single.gene.only = TRUE )
# show the BAM files
fls <- list.files (pattern='bam$', full=TRUE )
bamlst <- BamFileList(fls, index=character(), yieldSize=50000, obeyQname=TRUE )
#count reads overlapping bins
SE <- summarizeOverlaps (exonicParts, bamlst, mode='Union', singleEnd=FALSE, ignore.strand=TRUE, inter.feature=FALSE, fragments=TRUE )
colData (SE)$condition <- c("VP-35", "WT", "VP-35", "WT")
#Build DEXSeq Dataset
DEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon )
DEXSeq : Error in DESeqDataSet(rse, design, ignoreRank = TRUE
dxd <- DEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon )
dxd <- estimateSizeFactors (dxd )
dxd <- estimateDispersions (dxd )