Hi

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, but as far as I know I have changed my data into a matrix.

The dataset I have in my example of my run is only a small part. I have around 1000 rows in total. I have checked that none of the rows contains any letters etc, and I have removed the rows where some of the samples contain NA. So I can't see why the numbers aren't numeric.

I have tried to change the numbers to contain dots instead of commas, but this still gives me the same error.

I hope someone can give me a hint to what I am doing wrong!

I am still very new to R, and apologize in advance if this is just some simple stupid mistake.

My R run is this:

#Load in data
>data<-read.table("/Users/gban/Desktop/Probes_for_heatmap_35_meth_diff_both_hypo_and_hypermeth_Gene&probenames.txt",sep="\t",header=TRUE,row.names=1)



# Throw out rows with missing values.
>data = na.omit(data)



>data
                                  OS_Tumor1_08_14985_2_3 OS_Tumor2_08_226869_1
CHST3_cg04268405_1                           0,950380605            0,76433753
DLX5_cg19962750_2                             0,93111825           0,753845234
ZIC4_cg12892506_3                            0,860337466           0,696149332
DLX5_cg05597836_4                            0,906981714           0,664148911
ARHGEF7_cg09129334_6                          0,88102921           0,726231077
ZIC4_cg02387803_7                            0,770987986           0,568085839
ZIC4_cg05855917_8                            0,880514891           0,681148663
DLX5_cg13286614_9                            0,855132688           0,592368469
ZIC4_cg04556126_10                           0,907405655           0,718858033
LOC145845_cg25718467_11                      0,893492688           0,793191968
ZIC4_cg08393041_12                           0,911133787           0,678042743
SNED1_cg03785076_13                          0,862060883            0,70294155
C10orf116_cg01004363_14                      0,858555164           0,553920222
DLX5_cg20250426_15                           0,903165828            0,64976206
EPHX3_cg16184495_16                          0,927538308           0,519523714
SNED1_cg21304158_17                          0,762270611           0,647588457
EN1_cg12418535_19                            0,790529679           0,318880892
RTKN_cg00689340_20                           0,941714187           0,675243565
SNED1_cg16937168_21                          0,894421593           0,821448724
CD93_cg12873119_22                            0,86949625           0,676389091
RRN3P2_cg00525931_23                         0,862670615           0,855822961
GPBAR1_cg18581950_24                         0,800216557           0,810012301
SPARCL1_cg15552249_25                        0,815666773           0,837099021
HOXD12_cg23130254_26                         0,840109076           0,502896181
ZIC4_cg08889797_27                           0,779606392           0,591615859
ESRP2_cg06723863_28                          0,655488067            0,47819514
ZIC4_cg16790847_29                           0,735676228           0,611372155
PFDN5_cg16309127_30                          0,753348167           0,630504254
ARHGEF7_cg05776861_31                        0,951737748           0,926613919
TBX15_cg24720355_32                          0,906521431           0,364984479
FER1L5_cg01876130_33                         0,601084686           0,805388591
HOXD12_cg18022224_34                         0,865974739           0,543178066
DLX6AS_cg26251506_35                         0,804479354           0,538022928
GSTM5_cg05376982_36                          0,733426641           0,552089202
ZIC4_cg12976081_37                           0,464939006           0,551218578
HOXB4_cg02132714_38                          0,798491712           0,718121432
HOXD10_cg17489939_39                         0,970868858           0,790134913
C10orf116_cg12261786_40                      0,727394677           0,573072856
SPARCL1_cg19466563_41                         0,79754226           0,722582785
HOXD12_cg03964958_42                         0,778450531           0,679889139
HOXA5_cg09549073_43                            0,4652904           0,377825589
ZIC4_cg00334063_44                           0,783052842           0,634682328
TBX15_cg16990168_45                          0,893463329           0,235197972

#Load gplot package
>library(gplots)

#Make the data into a matrix
>data1<-as.matrix(data)

>data1

                                  OS_Tumor1_08_14985_2_3 OS_Tumor2_08_226869_1
CHST3_cg04268405_1                "0,950380605"          "0,76433753"
DLX5_cg19962750_2                 "0,93111825"           "0,753845234"
ZIC4_cg12892506_3                 "0,860337466"          "0,696149332"
DLX5_cg05597836_4                 "0,906981714"          "0,664148911"
ARHGEF7_cg09129334_6              "0,88102921"           "0,726231077"
ZIC4_cg02387803_7                 "0,770987986"          "0,568085839"
ZIC4_cg05855917_8                 "0,880514891"          "0,681148663"
DLX5_cg13286614_9                 "0,855132688"          "0,592368469"
ZIC4_cg04556126_10                "0,907405655"          "0,718858033"
LOC145845_cg25718467_11           "0,893492688"          "0,793191968"
ZIC4_cg08393041_12                "0,911133787"          "0,678042743"
SNED1_cg03785076_13               "0,862060883"          "0,70294155"
C10orf116_cg01004363_14           "0,858555164"          "0,553920222"
DLX5_cg20250426_15                "0,903165828"          "0,64976206"
EPHX3_cg16184495_16               "0,927538308"          "0,519523714"
SNED1_cg21304158_17               "0,762270611"          "0,647588457"
EN1_cg12418535_19                 "0,790529679"          "0,318880892"
RTKN_cg00689340_20                "0,941714187"          "0,675243565"
SNED1_cg16937168_21               "0,894421593"          "0,821448724"
CD93_cg12873119_22                "0,86949625"           "0,676389091"
RRN3P2_cg00525931_23              "0,862670615"          "0,855822961"
GPBAR1_cg18581950_24              "0,800216557"          "0,810012301"
SPARCL1_cg15552249_25             "0,815666773"          "0,837099021"
HOXD12_cg23130254_26              "0,840109076"          "0,502896181"
ZIC4_cg08889797_27                "0,779606392"          "0,591615859"
ESRP2_cg06723863_28               "0,655488067"          "0,47819514"
ZIC4_cg16790847_29                "0,735676228"          "0,611372155"
PFDN5_cg16309127_30               "0,753348167"          "0,630504254"
ARHGEF7_cg05776861_31             "0,951737748"          "0,926613919"
TBX15_cg24720355_32               "0,906521431"          "0,364984479"
FER1L5_cg01876130_33              "0,601084686"          "0,805388591"
HOXD12_cg18022224_34              "0,865974739"          "0,543178066"
DLX6AS_cg26251506_35              "0,804479354"          "0,538022928"
GSTM5_cg05376982_36               "0,733426641"          "0,552089202"
ZIC4_cg12976081_37                "0,464939006"          "0,551218578"
HOXB4_cg02132714_38               "0,798491712"          "0,718121432"
HOXD10_cg17489939_39              "0,970868858"          "0,790134913"
C10orf116_cg12261786_40           "0,727394677"          "0,573072856"
SPARCL1_cg19466563_41             "0,79754226"           "0,722582785"
HOXD12_cg03964958_42              "0,778450531"          "0,679889139"
HOXA5_cg09549073_43               "0,4652904"            "0,377825589"
ZIC4_cg00334063_44                "0,783052842"          "0,634682328"
TBX15_cg16990168_45               "0,893463329"          "0,235197972"

heatmap.2(data1, col=redgreen(75), scale="row", key=T, keysize=1.5,density.info="none", trace="none",cexCol=0.9, labRow=NA)
Fejl i heatmap.2(data1, col = redgreen(75), scale = "row", key = T,  :
  `x' must be a numeric matrix

Many thanks!

Kind regards

Gitte Brinch Andersen


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