MissMDA error message

[Emily Choy]

Dear Factominer users,

I am having trouble using missMDA to imput missing PCA values.  I have a table of fatty acid proportions that have been log transformed.
When I put in the first line of code :

nb <- estim_ncpPCA(orange,ncp.min=0, ncp.max=5)
 
I get:

Error in eigen(crossprod(X, X), symmetric = TRUE) :
  infinite or missing values in 'x'

Also, is it possible to use missMDA for a PCA if you have qualitative supplementary variables?

Thank you,
Emily

[François Husson]

Hi,

If you have continuous and categorical variables, and you want to use only the continuous variables as active variables, you should omit first the categorical variables, impute the continuous variables and then concatenate the imputed dataset and the categorical variables.

Else, if you want to use all the variables as active variables, you should use the imputeFAMD function. This function will use both continuous and categorical variables to impute missing values.

Best

FH

[Raquel Pereira]

Hej 

I am having the same issue, with all my variables being continuous. 

I have some zeros (actual number 0) and some NA, I was trying to get the estim_ncpPCA to work, but without success.

variables<-estim_ncpPCA(trim.data,ncp.min=0, ncp.max=5)

estim_ncpPCA(trim.data, ncp.min=0,ncp.max=3)

Error in eigen(crossprod(t(X), t(X)), symmetric = TRUE) : 

  infinite or missing values in 'x'

head(trim.data,3)

                                           Length_mega_1 Length_mega_2 Length_mega_3 Length_mega_4 Length_mega_5  .... Length_mega_36

BMNH_1954_3_9_425             284.3                    185.8                  272.5                   311.4                338.2

BR513                                       408.1                     335.1                 402.7                  427.3                332.4

P056_111012_1                        390.0                     380.0                  365.0                 350.0                 330.0

What am I doing wrong?

[Raquel Pereira]

NOTE

trim.data[1,1]

[1] 284.3

On Saturday, November 28, 2015 at 10:19:19 PM UTC+1, Emily Choy wrote:

[josse]

Dear Raquel and Emily,

Could you send me the summary of your data so that I can get a hint on what's going on,

Best wishes,

Julie

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[Daniel Pinillos]

Hi Raquel,

I am having the exact same problem, I have some 0s and some NAs in my data and I get the same message over and over. Did you find out what was wrong or an alternative solution? (I am trying to run a PCA with missing values)

Thanks!!

Daniel

[François Husson]

The problem was that one of the variable has only NA except just one observed value. So the standard deviation cannot be calculated. It is necessary to suppress this variable ... and then everything will be ok!

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Department Statistics & Computer science
AGROCAMPUS OUEST
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Tel: +33 2 23 48 58 86
https://husson.github.io

[Cecilia Alonso]

hi Francois,

Iam having the same problem while trying to impute missing data with missMDA. I get this error ( Error in eigen(crossprod(X, X), symmetric = TRUE) : infinite or missing values in 'x'), even when there is only one variable with NAs and there are only 2 NAs in 30 observations... attached goes the csv file.

many thanks in advance for your help!

best regards

Cecilia

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[Francois Husson]

Hi,

Your variable depth is not a variable because there are only 0. Thus it is not possible to use this column whin is not a variable. The standard deviation is 0, and thus you cannot perform a standardized PCA.

So suppress this column from your dataset.

FH

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Department Statistics & Computer science

IRMAR 6625
65 rue de St-Brieuc - Agrocampus Ouest - 35042 RENNES

Tel: +33 2 23 48 58 86

https://husson.github.io/

[Cecilia Alonso]

hi, thank you very much. I had suppressed it in other analyses, but not in this one :(

sorry for the mistake.

best regards

Cecilia

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[SHAMIHAH GHAZALI]

Hi Francois, i have been use this missmda package and load for imputing missing values using imputePCA function and do some simulating pattern (up to 100 array) of missingness to be imputed. but when i load some of simulation along with the imputePCA function it show some error which is

" Error in eigen(crossprod(X, X), symmetric = TRUE) : 

  infinite or missing values in 'x' "

if you want to see my data pet me get your email and i will email personally to you. Thankyou

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[Francois Husson]

Maybe you have some individuals or some wariabes that only have missing values.

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[SHAMIHAH GHAZALI]

Thankyou so much for the replies! i had found the problem..some of the array have only missing values then the standard deviation cant be calculated. 

Best Regards,

Shamihah Binti Muhammad Ghazali

Sarjana Sains Statistik (CS753)

Fakulti Sains Komputer & Matematik

Universiti Teknologi MARA, Shah Alam

(011-25613411)

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