Question: Issue with DESeq: unable to find an inherited method for function (exprs) for signature DESeqTransform
0
gravatar for catglen012
16 months ago by
catglen01210
catglen01210 wrote:

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?

rna-seq deseq R • 1.6k views
ADD COMMENTlink modified 16 months ago by WouterDeCoster42k • written 16 months ago by catglen01210
2
gravatar for WouterDeCoster
16 months ago by
Belgium
WouterDeCoster42k wrote:

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))
ADD COMMENTlink written 16 months ago by WouterDeCoster42k

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

ADD REPLYlink written 16 months ago by Kevin Blighe53k

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

ADD REPLYlink written 16 months ago by catglen01210

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 16 months ago by Kevin Blighe53k
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