DESeq2 Glimma2 visualisation error
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Entering edit mode
11 months ago
Pahi ▴ 10

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!

DESeq2 Glimma2 Plot R • 621 views
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Entering edit mode

Same problem here, did you manage to solve it somehow?

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I changed to edger for my analysis, becouse later on with deseq I had a lot of other issues.

If I remember correcly, in glimma you have to define some parameters manually. For my edger input it looks like:

Glimma::glimmaMA(edger_data, dge = y), where edger_data is an lrt list of my data, which is separated from the original edger output.

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