[R] lars - lasso problem
Steve Lianoglou
mailinglist.honeypot at gmail.com
Fri Apr 8 20:01:22 CEST 2011
Hi,
First: Please make sure you CC R-help when responding to messages on
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Now:
Look at the help for the lars function:
R> ?lars
You'll see that `x` should be a matrix. I guess it doesn't say as
much, but `y` should be a (numeric) response.
Both of x and y in your case are data.frames. Convert them to the
appropriate objects and try again, eg:
R> x <- as.matrix(x)
R> y <- as.numeric(y[,1])
Now make sure that these objects look right by (among other things)
examining the output of:
R> head(x)
R> head(y)
Then try lars again.
Also, I'd suggest using the glmnet package instead of lars. It's
written by the same people and you'll get both the lasso and
elasticnet under one roof.
-steve
On Fri, Apr 8, 2011 at 1:54 PM, gauri j <gauri.jape7 at gmail.com> wrote:
> hi,
> the output of commands given by you, is as follows,
>
>
> command:
> R> is(x)
> R> apply(x, 2, function(x) is(x)[1])
> R> is(y)
>
>
>
> output:
> is(x)
> [1] "data.frame" "list" "oldClass" "vector"
>> apply(x, 2, function(x) is(x)[1])
> V1 V2 V3 V4 V5 V6 V7
> V8
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V9 V10 V11 V12 V13 V14 V15
> V16
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V17 V18 V19 V20 V21 V22 V23
> V24
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V25 V26 V27 V28 V29 V30 V31
> V32
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V33 V34 V35 V36 V37 V38 V39
> V40
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V41 V42 V43 V44 V45 V46 V47
> V48
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V49 V50 V51 V52 V53 V54 V55
> V56
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V57 V58 V59 V60 V61 V62 V63
> V64
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V65 V66 V67 V68 V69 V70 V71
> V72
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V73 V74 V75 V76 V77 V78 V79
> V80
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V81 V82 V83 V84 V85 V86 V87
> V88
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V89 V90 V91 V92 V93 V94 V95
> V96
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V97 V98 V99 V100 V101 V102 V103
> V104
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V105 V106 V107 V108 V109 V110 V111
> V112
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V113 V114 V115 V116 V117 V118 V119
> V120
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V121 V122 V123 V124 V125 V126 V127
> V128
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V129 V130 V131 V132 V133 V134 V135
> V136
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V137 V138 V139 V140 V141 V142 V143
> V144
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V145 V146 V147 V148 V149 V150 V151
> V152
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V153 V154 V155 V156 V157 V158 V159
> V160
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V161 V162 V163 V164 V165 V166 V167
> V168
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V169 V170 V171 V172 V173 V174 V175
> V176
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V177 V178 V179 V180 V181 V182 V183
> V184
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V185 V186 V187 V188 V189 V190 V191
> V192
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V193 V194 V195 V196 V197 V198 V199
> V200
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V201 V202 V203 V204 V205 V206 V207
> V208
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V209 V210 V211 V212 V213 V214 V215
> V216
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V217 V218 V219 V220 V221 V222 V223
> V224
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V225 V226 V227 V228 V229 V230 V231
> V232
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V233 V234 V235 V236 V237 V238 V239
> V240
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V241 V242 V243 V244 V245 V246 V247
> V248
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V249 V250 V251 V252 V253 V254 V255
> V256
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V257 V258 V259 V260 V261 V262 V263
> V264
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V265 V266 V267 V268 V269 V270 V271
> V272
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
> V273 V274 V275 V276 V277 V278 V279
> V280
> "integer" "integer" "integer" "integer" "integer" "integer" "integer"
> "integer"
>> is(y)
> [1] "data.frame" "list" "oldClass" "vector"
>
> On Fri, Apr 8, 2011 at 11:11 AM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>>
>> Hi,
>>
>> On Fri, Apr 8, 2011 at 10:33 AM, gauri j <gauri.jape7 at gmail.com> wrote:
>> > hi,
>> > I have problem in following code, error is occurred. I have attached my
>> > data
>> > herewith. and my code is as following,
>> >> library(lars)
>> > Loaded lars 0.9-8
>> > Warning message:
>> > package 'lars' was built under R version 2.12.2
>> >> x<- read.table("D:/spring '11/james reggression/NewFeature.txt")
>> >> y<-read.table("D:/spring '11/lars/RFU.txt")
>> >> out<- lars(x,y, type = "lasso")
>> > Error in one %*% x : requires numeric/complex matrix/vector arguments
>>
>> What is the output for the following commands?
>>
>> R> is(x)
>> R> apply(x, 2, function(x) is(x)[1])
>> R> is(y)
>>
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>> | Memorial Sloan-Kettering Cancer Center
>> | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
>
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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