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lpantano avatar lpantano commented on June 12, 2024

Hi,

hum, normally that happens when colData(dds)['station'] is not a factor. can you check what class(colData(dds)['station']) is giving to you?

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elcega avatar elcega commented on June 12, 2024 
class(colData(dds)['station'])
[1] "DFrame"
attr(,"package")
[1] "S4Vectors"
colData(dds)['station'] = as.factor(colData(dds)['station'])
Error in as.vector(x, mode = "character") : 
  no method for coercing this S4 class to a vector
>

I am running the following code:

res <- degPatterns(df3, metadata = colData(dds), time = "station", minc = 5)
degPlotCluster(res$normalized, "station")

For which I obtain the following:

Working with 1312 genes.
Working with 1311 genes after filtering: minc > 5
Joining, by = "merge"
Joining, by = "merge"
geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic?
geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic?
...

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mbrochut avatar mbrochut commented on June 12, 2024

I had the same issue and as @lpantano said, the probleme comes from the column used in "time" from the metadata, is not a factor!
If another person find this, you can follow another answer from @lpantano to transform your column into factor: #39 (comment)

Here is the quick solution:
your_metadata$column_used_in_time = as.factor(your_metadata$column_used_in_time)

It should do the trick :)

ps: thank you @lpantano

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