Error with ropls when using oplsda: Error in svd(wwMN) : infinite or missing values in 'x'
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g0079 • 0
@e1ad402a
Last seen 21 months ago
China

Hi, I,m learning ropls to analysis my own metabolomics data. Thanks to ropls, I can do PCA ans PLS-DA successfully. But when I tried to use OPLS-DA method with the following code, the error occured as "Error in svd(wwMN) : infinite or missing values in 'x'". I'm sure that there is no NA, Inf and even 0 in my data, and I don't know how to deal with it. Could you help to see the reason for this error? Thank you very much.

```r caasTibOplsda #data uesd to learn ropls

A tibble: 8 × 1,870

V10001 V10004 V10043 V10047 V10049 V10051 V10060 V10076 V10081 V10109 V10117 V10118 V10121 V10131 V10151 <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> 1 0.0580 0.0733 0.0821 0.0297 0.107 0.0347 0.203 0.0247 0.0379 0.106 0.0363 0.0313 0.327 0.0316 0.0663 2 0.0658 0.0996 0.295 0.0921 0.164 0.0417 0.034 0.0138 0.0344 0.0282 0.122 0.0944 0.170 0.0286 0.0553 3 0.0543 0.0006 0.0864 0.0313 0.105 0.0376 0.240 0.0313 0.0291 0.120 0.0387 0.0302 0.327 0.0484 0.0738 4 0.181 0.287 0.250 0.0866 0.141 0.0361 0.0354 0.0121 0.0373 0.0255 0.111 0.0844 0.157 0.0277 0.053 5 0.0538 0.0632 0.0859 0.0296 0.0882 0.0283 0.227 0.0287 0.0307 0.117 0.0391 0.0317 0.327 0.058 0.0692 6 0.217 0.324 0.288 0.0825 0.148 0.0357 0.0361 0.0134 0.0347 0.022 0.100 0.0872 0.142 0.0241 0.0571 7 0.0382 0.0602 0.0968 0.0339 0.106 0.0315 0.243 0.0243 0.0306 0.125 0.0413 0.0372 0.339 0.0447 0.065 8 0.125 0.170 0.267 0.0839 0.141 0.0361 0.0342 0.0116 0.0331 0.0248 0.110 0.0872 0.148 0.021 0.0503

… with 1,855 more variables: V10173 <dbl>, V10186 <dbl>, V10187 <dbl>, V10188 <dbl>, V10189 <dbl>,

V10190 <dbl>, V10195 <dbl>, V10198 <dbl>, V10199 <dbl>, V10214 <dbl>, V10222 <dbl>, V10226 <dbl>,

V10275 <dbl>, V10291 <dbl>, V10318 <dbl>, V10325 <dbl>, V10327 <dbl>, V10336 <dbl>, V10338 <dbl>,

V10346 <dbl>, V10349 <dbl>, V10352 <dbl>, V10353 <dbl>, V10357 <dbl>, V10370 <dbl>, V10376 <dbl>,

V10377 <dbl>, V10379 <dbl>, V1038 <dbl>, V1039 <dbl>, V104 <dbl>, V1040 <dbl>, V10413 <dbl>,

V10437 <dbl>, V10448 <dbl>, V10449 <dbl>, V10452 <dbl>, V10453 <dbl>, V1046 <dbl>, V10465 <dbl>,

V10472 <dbl>, V10473 <dbl>, V10474 <dbl>, V10475 <dbl>, V10498 <dbl>, V10515 <dbl>, V10542 <dbl>, …

groupOplsda #group information [1] SamA SamB SamA SamB SamA SamB SamA SamB Levels: SamA SamB SamC SamD

caasOplsda = opls(caasTibOplsda, groupOplsda, predI = 1, orthoI = NA) Error in svd(wwMN) : infinite or missing values in 'x'

ropls • 1.0k views
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Entering edit mode
g0079 • 0
@e1ad402a
Last seen 21 months ago
China

I found the reason, the levels of groupOplsda was wrong. When I modified the levels, it can work well.

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