Question

Heatmap with error message: `x' must be a numeric matrix

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Biologist ▴ 120

@biologist-9801

Last seen 4.7 years ago

Hi everyone,

I am trying to do a heatmap, but I can't see what I am doing wrong. I get the error message: `x' must be a numeric matrix.

library(limma)
library(Biobase)

setwd("/export/work/geneSTdataset")

expr.rma <- read.table("tmp_exonRMA.txt",dec = ",")

minimalSet <- new("ExpressionSet", exprs = as.matrix(expr.rma))

vv <- minimalSet[1:44797,1:6]

exprs(vv)
heatmap(exprs(vv))

Error:

Error in heatmap(exprs(vv)) : 'x' must be a numeric matrix

r heatmap numericmatrix • 21k views

ADD COMMENT • link updated 8.7 years ago by Assa Yeroslaviz ★ 1.5k • written 8.7 years ago by Biologist ▴ 120

score 2 · Answer 1 · 2016-03-15

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Assa Yeroslaviz ★ 1.5k

@assa-yeroslaviz-1597

Last seen 29 days ago

Germany

Why do you want to change it to an expressionSet, just to re-format it into a matrix?

Why not do it directly?

library(readr)

data <- read_tsv("tmp.txt") # read the exprs.rma object you gave as an example 

heatmap(as.matrix(data[,3:8])) # I assume you don't want to plot the ID columns (1:2)

this works.

ADD COMMENT • link 8.7 years ago Assa Yeroslaviz ★ 1.5k

score 0 · Answer 2 · 2016-03-15

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b.nota ▴ 370

@bnota-7379

Last seen 4.2 years ago

Netherlands

try

heatmap(as.matrix(exprs(vv)))

ADD COMMENT • link 8.7 years ago b.nota ▴ 370

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Yes, I tried that too before. But it didnt work.

ADD REPLY • link 8.7 years ago Biologist ▴ 120

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I have the following data in text file:

UNIT_ID   UnitName   X_8__HuGene_2_0_st_.mdp_LEVEL   E__HuGene_2_0_st_.mdp_LEVEL   GG7__HuGene_2_0_st_.mdp_LEVEL   J__HuGene_2_0_st_.mdp_LEVEL   O__HuGene_2_0_st_.mdp_LEVEL   T__HuGene_2_0_st_.mdp_LEVEL
0   17127159   353.568   335.295   221.717   815.654   684.85   803.736
1   17127161   11.0842   7.01459   7.33511   11.2121   12.6268   10.3683
2   17127163   221.647   226.774   136.274   431.32   392.533   704.743
3   17127165   5.02182   3.41172   4.12834   6.90306   4.91183   5.65681
4   17127167   393.915   433.671   228.328   1083.58   695.285   830.416
5   17127169   7.38325   6.0512   4.32289   6.09091   4.60186   5.88536
6   17127171   497.88   424.125   281.876   1349.68   772.386   920.554
7   17127173   10.9418   5.62108   5.58565   6.4397   4.55153   6.67684

ADD REPLY • link 8.7 years ago Biologist ▴ 120

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Can you show me?:

head(vv)

ADD REPLY • link 8.7 years ago b.nota ▴ 370

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ExpressionSet (storageMode: lockedEnvironment)
assayData: 1 features, 6 samples 
  element names: exprs 
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'
Annotation:

ADD REPLY • link 8.7 years ago Biologist ▴ 120

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what do you get when you do

str(exprs(vv))

Are you sure it has a matrix structure?

ADD REPLY • link 8.7 years ago Assa Yeroslaviz ★ 1.5k

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It looks like you only have one feature in your assayData

ADD REPLY • link 8.7 years ago b.nota ▴ 370

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chr [1:44797, 1:6] "UNIT_ID" "0" "1" "2" "3" "4" "5" "6" "7" ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:44797] "1" "2" "3" "4" ...
  ..$ : chr [1:6] "V1" "V2" "V3" "V4" ...

Yes, I have only one feature. So, how to get a heatmap now?

ADD REPLY • link 8.7 years ago Biologist ▴ 120

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Get more features!

ADD REPLY • link 8.7 years ago b.nota ▴ 370