Heatmap with error message: `x' must be a numeric matrix
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Biologist ▴ 90
@biologist-9801
Last seen 13 months 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 • 16k views
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 3 days ago
Munich, 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.

 

 

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b.nota ▴ 340
@bnota-7379
Last seen 7 months ago
Netherlands

try

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

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

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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

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Can you show me?:

head(vv)

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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:  
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what do you get when you do

str(exprs(vv))

Are you sure it has a matrix structure?

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It looks like you only have one feature in your assayData

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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? 

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