Error from DegPlot $<-.data.frame(*tmp*, "xs", value = integer(0)) : replacement has 0 rows, data has 96 1 0 Entering edit mode kavator ▴ 20 @kavator-22955 Last seen 3 months ago Hi Lorraine/folks I have previously managed to use DegPlot as you have know. However, just now when I run similar chunk, it gives me the output of - which I have trouble interpreting what it means. my goal is to see how the top genes varies across all my sample groups Could you give me a clue? thanks Error in $<-.data.frame(*tmp*, "xs", value = integer(0)) : replacement has 0 rows, data has 96


The chunk that was ran (it was a 2x2 factorial):

dds <- DESeqDataSet(gse, design = ~ gender*treatment)
dds <- DESeq(dds)
res<-results(dds)
degPlot(dds, res=res, n=10, xs = "group",group="group",groupLab = "sampletype",ann = c("gene_id","symbol"),color="Accent")


Intuitively, i think it has something to do with the group variable. However, I was wondering if the group variable is automatically extracted/defined from the dds/res? thanks

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2
Entering edit mode
@kevin
Last seen 3 hours ago
Naas, Republic of Ireland

Hey,

You need to verify that 'group' is a column name in colData(dds) - also check its encoding (character or factor?).

Also check that the following is true for ann`:

ann

Columns in rowData (if available) used to print gene names. First element in the vector is the column name in rowData that matches the row.names of the dds or count object. Second element in the vector is the column name in rowData that it will be used as the title for each gene or feature figure.

Kevin

1
Entering edit mode

thanks Kevin managed to resolve it with your suggestions