EdgeR annotation
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@gordon-smyth
Last seen 23 minutes ago
WEHI, Melbourne, Australia
Dear Robin, I don't think the problem is with edgeR. You are setting genes=data[,0:1] However there is no column 0, so 0:1 reduces to column 1, which is being set as annotation. But you also input column 1 as a count: counts=data[,1:18] These can't both be right. I suspect you just want: y <- DGEList(counts=data) Best wishes Gordon ----- original message ------ [R] EdgeR annotation Robin Mjelle robinmjelle at gmail.com Sat Aug 24 13:50:55 CEST 2013 after updating R and edgeR I lost the annotations in the final Diff.Expressed matrix (toptags) when running the edgeR pipeline. How do I get the row.names from the data matrix into the topTag-matrix? data <- read.table("KO_and_WT_Summary_miRNA_Expression.csv", row.names=1, sep="", header=T) keep <- rowSums(cpm(data)>2) >=2 data <- data[keep, ] table(keep) y <- DGEList(counts=data[,1:18], genes=data[,0:1]) y <- calcNormFactors(y) y$samples plotMDS(y,main="") Time=c("0.25h","0.5h","1h","2h","3h","6h","12h","24h","48h","0.25h","0 .5h","1h","2h","3h","6h","12h","24h","48h") Condition=c("KO","KO","KO","KO","KO","KO","KO","KO","KO","WT","WT","WT ","WT","WT","WT","WT","WT","WT") design <- model.matrix(~0+Time+Condition) rownames(design) <- colnames(y) y <- estimateGLMCommonDisp(y, design, verbose=TRUE, method="deviance",robust=TRUE, subset=NULL) y <- estimateGLMTrendedDisp(y, design) y <- estimateGLMTagwiseDisp(y, design) fit <- glmFit(y, design) lrt <- glmLRT(fit) topTags(lrt) Coefficient: ConditionWT genes logFC logCPM LR PValue FDR 189 5128 -11.028422 7.905804 4456.297 0 0 188 12271 -10.582267 9.061326 5232.075 0 0 167 121120 -9.831894 12.475576 5957.104 0 0 34 255235 -9.771266 13.592968 7355.592 0 0 168 311906 -9.597952 13.907951 10710.111 0 0 166 631262 -9.592550 14.932018 11719.222 0 0 79 79 9.517226 11.466696 7964.269 0 0 169 2512 -8.946429 6.758584 2502.548 0 0 448 3711 -7.650068 7.764682 2914.784 0 0 32 260769 -7.412197 13.633352 4906.198 0 0 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
Annotation edgeR Annotation edgeR • 1.3k views
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