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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