I’m working on my RNA-seq pipeline, with deseq2, and I would like to use Glimma2, for interactive visualisation. My problem is that, after I do the DESeq analysation, I can’t plot it. On different sites, It is said, that it is as simple as: glimmaMA(dds)
But I get the following error:
Error in buildXYData(table, status, main, display.columns, anno, counts, :
Length of groups must be equal to the number of columns in counts.
So far I tried adding annotation to my dds with:
annot <- mapIds(EnsDb.Hsapiens.v86, gene_id, keytype = "GENEID", column="SYMBOL",multiVals="first")
Where gene_id contains all my id-s. But still, I get the error.
Here is my code:
library(DESeq2)
counts <- mydata.txt
conditions <- factor(c(rep("untreated", 3), rep("treated", 3)))
coldata <- data.frame(row.names=colnames(Counts), conditions)
dds_data <- DESeqDataSetFromMatrix(countData = Counts,
colData = coldata,
rowData = gene_id,
design = ~ conditions)
annot <- mapIds(EnsDb.Hsapiens.v86, gene_id, keytype = "GENEID", column="SYMBOL",multiVals="first")
keep <- rowSums(counts(dds_data)) >= 10
dds_data <- dds_data[keep,]
dds <- DESeq(dds)
mcols(dds) <- DataFrame(annot)
res <- results(dds, contrast=c("conditions","treated","untreated"))
resultsNames(dds)
resLFC <- lfcShrink(dds, coef="conditions_untreated_vs_treated", type="apeglm")
resOrdered <- res[order(res$pvalue),]
plotMA(res, ylim=c(-2,2)) #working
plotMA(resLFC, ylim=c(-2,2)) #working
library(Glimma)
glimmaMDS(dds) #working
glimmaMA(dds)
glimmaVolcano(dds)
glimmaMA(dds)
43467 of 60605 genes were filtered out in DESeq2 tests
Error in buildXYData(table, status, main, display.columns, anno, counts, :
Length of groups must be equal to the number of columns in counts.
What could be the problem? Thank you in advance!
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