Issue with DESeq: unable to find an inherited method for function (exprs) for signature DESeqTransform

Question

[catglen012]

Hello! I am trying to create a heatmap but I am unable to do so because it seems like an object "exprs" is masked:

> heatmap.2(exprs(vsdFull)[select,], col = hmcol, trace="none", margin=c(10, 6))

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘exprs’ for signature ‘"DESeqTransform"’

I was wondering what do I need to type in my console for this error not to occur?

Answer 1

[WouterDeCoster]

The error is quite descriptive of what is wrong. The function exprs() doesn't work because it does not recognise the vsdFull object, which is a "DESeqTransform". You need to access the counts inside that object:

heatmap.2(assay(vsdFull)[select,], col = hmcol, trace="none", margin=c(10, 6))

[Kevin Blighe]

To add, exprs() is applied to ExpressionSet objects, which usually contain gene expression microarray data.

[catglen012]

I was not sure of what it meant since I am following a tutorial/ beginner, but thank you so much! This solved my problem!

[Kevin Blighe]

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