error with as.numeric when running pvclust
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Alyaa Mahmoud ▴ 440
@alyaa-mahmoud-4670
Last seen 19 months ago
Dear All I have a dataframe (data) with numeric values. However, when I run pvclust i get the error: > pv <- pvclust(as.matrix(data), method.dist="correlation", method.hclust="complete", nboot=10) Error in cor(x, method = "pearson", use = use.cor) : 'x' must be numeric I tried to convert to numeric using as.numeric: data[,1:5] = lapply(data[,1:5], as.numeric) but the values change if I do this ????? Anybody knows why would the values change when I use as.numeric ?? How can I convert the values to "numeric" without changing them then ?? > data TCGA.02.0074.01A.01R.0202.01 TCGA.06.0174.01A.01R.0233.01 1053_at *6.78057386468964* 7.20429615680331 117_at 4.5369738739652 5.71461488261629 121_at 5.7547177840092 6.27768302308676 1255_g_at 3.51242959009833 4.38185514015951 1294_at 5.71812084213166 5.18297525921706 TCGA.06.0188.01A.01R.0233.01 TCGA.06.0241.01A.02R.0233.01 1053_at 6.32600010999327 7.36481160075073 117_at 4.8915996267868 4.91877155427287 121_at 6.22521524027822 5.92939849291023 1255_g_at 5.81450662569868 3.56178691911277 1294_at 5.94603190363047 5.08045063963826 TCGA.06.0178.01A.01R.0233.01 1053_at 7.08406595975373 117_at 4.45519578310485 121_at 6.98951423954871 1255_g_at 3.41240570036661 1294_at 6.19723107114317 > pv <- pvclust(as.matrix(data), method.dist="correlation", method.hclust="complete", nboot=10) Error in cor(x, method = "pearson", use = use.cor) : 'x' must be numeric > *data[,1:5] = lapply(data[,1:5], as.numeric)* > data TCGA.02.0074.01A.01R.0202.01 TCGA.06.0174.01A.01R.0233.01 1053_at *15129 * 16227 117_at 9527 12658 121_at 12662 13992 1255_g_at 2970 8963 1294_at 12578 11398 TCGA.06.0188.01A.01R.0233.01 TCGA.06.0241.01A.02R.0233.01 1053_at 14118 16721 117_at 10585 10885 121_at 13874 13334 1255_g_at 12852 2937 1294_at 13197 11307 TCGA.06.0178.01A.01R.0233.01 1053_at 16314 117_at 8829 121_at 16074 1255_g_at 1765 1294_at Thanks a lot yours, Alyaa -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 4 hours ago
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Hi Alyaa, See here: http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-do-I-convert-factors- to-numeric_003f Best, Jim On 11/13/2012 1:52 PM, Alyaa Mahmoud wrote: > Dear All > > I have a dataframe (data) with numeric values. However, when I run pvclust > i get the error: > >> pv<- pvclust(as.matrix(data), method.dist="correlation", > method.hclust="complete", nboot=10) > Error in cor(x, method = "pearson", use = use.cor) : 'x' must be numeric > > I tried to convert to numeric using as.numeric: > data[,1:5] = lapply(data[,1:5], as.numeric) but the values change if I do > this ????? > > Anybody knows why would the values change when I use as.numeric ?? How can > I convert the values to "numeric" without changing them then ?? > >> data > TCGA.02.0074.01A.01R.0202.01 TCGA.06.0174.01A.01R.0233.01 > 1053_at *6.78057386468964* 7.20429615680331 > 117_at 4.5369738739652 5.71461488261629 > 121_at 5.7547177840092 6.27768302308676 > 1255_g_at 3.51242959009833 4.38185514015951 > 1294_at 5.71812084213166 5.18297525921706 > TCGA.06.0188.01A.01R.0233.01 TCGA.06.0241.01A.02R.0233.01 > 1053_at 6.32600010999327 7.36481160075073 > 117_at 4.8915996267868 4.91877155427287 > 121_at 6.22521524027822 5.92939849291023 > 1255_g_at 5.81450662569868 3.56178691911277 > 1294_at 5.94603190363047 5.08045063963826 > TCGA.06.0178.01A.01R.0233.01 > 1053_at 7.08406595975373 > 117_at 4.45519578310485 > 121_at 6.98951423954871 > 1255_g_at 3.41240570036661 > 1294_at 6.19723107114317 >> pv<- pvclust(as.matrix(data), method.dist="correlation", > method.hclust="complete", nboot=10) > Error in cor(x, method = "pearson", use = use.cor) : 'x' must be numeric >> *data[,1:5] = lapply(data[,1:5], as.numeric)* >> data > TCGA.02.0074.01A.01R.0202.01 TCGA.06.0174.01A.01R.0233.01 > 1053_at *15129 * 16227 > 117_at 9527 12658 > 121_at 12662 13992 > 1255_g_at 2970 8963 > 1294_at 12578 11398 > TCGA.06.0188.01A.01R.0233.01 TCGA.06.0241.01A.02R.0233.01 > 1053_at 14118 16721 > 117_at 10585 10885 > 121_at 13874 13334 > 1255_g_at 12852 2937 > 1294_at 13197 11307 > TCGA.06.0178.01A.01R.0233.01 > 1053_at 16314 > 117_at 8829 > 121_at 16074 > 1255_g_at 1765 > 1294_at > > > Thanks a lot > yours, > Alyaa -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi James Thanks a lot for that. I also found out that I could use stringsAsFactors=FALSE in the read.table command. I appologize for reposting an already answered question. Thanks a lot yours, Alyaa On Tue, Nov 13, 2012 at 9:45 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Alyaa, > > See here: > > http://cran.r-project.org/doc/**FAQ/R-FAQ.html#How-do-I-** > convert-factors-to- numeric_**003f<http: cran.r-project.org="" doc="" faq="" r-faq.html#how-do-i="" -convert-factors-to-numeric_003f=""> > > Best, > > Jim > > > > > On 11/13/2012 1:52 PM, Alyaa Mahmoud wrote: > >> Dear All >> >> I have a dataframe (data) with numeric values. However, when I run pvclust >> i get the error: >> >> pv<- pvclust(as.matrix(data), method.dist="correlation", >>> >> method.hclust="complete", nboot=10) >> Error in cor(x, method = "pearson", use = use.cor) : 'x' must be numeric >> >> I tried to convert to numeric using as.numeric: >> data[,1:5] = lapply(data[,1:5], as.numeric) but the values change if I do >> this ????? >> >> Anybody knows why would the values change when I use as.numeric ?? How can >> I convert the values to "numeric" without changing them then ?? >> >> data >>> >> TCGA.02.0074.01A.01R.0202.01 TCGA.06.0174.01A.01R.0233.01 >> 1053_at *6.78057386468964* 7.20429615680331 >> >> 117_at 4.5369738739652 5.71461488261629 >> 121_at 5.7547177840092 6.27768302308676 >> 1255_g_at 3.51242959009833 4.38185514015951 >> 1294_at 5.71812084213166 5.18297525921706 >> TCGA.06.0188.01A.01R.0233.01 TCGA.06.0241.01A.02R.0233.01 >> 1053_at 6.32600010999327 7.36481160075073 >> 117_at 4.8915996267868 4.91877155427287 >> 121_at 6.22521524027822 5.92939849291023 >> 1255_g_at 5.81450662569868 3.56178691911277 >> 1294_at 5.94603190363047 5.08045063963826 >> TCGA.06.0178.01A.01R.0233.01 >> 1053_at 7.08406595975373 >> 117_at 4.45519578310485 >> 121_at 6.98951423954871 >> 1255_g_at 3.41240570036661 >> 1294_at 6.19723107114317 >> >>> pv<- pvclust(as.matrix(data), method.dist="correlation", >>> >> method.hclust="complete", nboot=10) >> Error in cor(x, method = "pearson", use = use.cor) : 'x' must be numeric >> >>> *data[,1:5] = lapply(data[,1:5], as.numeric)* >>> data >>> >> TCGA.02.0074.01A.01R.0202.01 TCGA.06.0174.01A.01R.0233.01 >> 1053_at *15129 * 16227 >> >> 117_at 9527 12658 >> 121_at 12662 13992 >> 1255_g_at 2970 8963 >> 1294_at 12578 11398 >> TCGA.06.0188.01A.01R.0233.01 TCGA.06.0241.01A.02R.0233.01 >> 1053_at 14118 16721 >> 117_at 10585 10885 >> 121_at 13874 13334 >> 1255_g_at 12852 2937 >> 1294_at 13197 11307 >> TCGA.06.0178.01A.01R.0233.01 >> 1053_at 16314 >> 117_at 8829 >> 121_at 16074 >> 1255_g_at 1765 >> 1294_at >> >> >> Thanks a lot >> yours, >> Alyaa >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]
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