Question: EIGENSOFT: CONVERTF ignoring samples
gravatar for aritra90
3.1 years ago by
United States
aritra9020 wrote:

Hi, the CONVERTF program in EIGENSOFT package is ignoring few samples and not calculating their principal components. 

I am seeing this in my terminal when executing CONVERTF. 

genetic distance set from physical distance

Sample1 ignored
Sample2 ignored
Sample3 ignored


Samplen ignored

genotype file processed
numvalidind:     21  maxmiss: 21001
packedancestrymap output
##end of convertf run

Usually, it says ignoring all samples and then outputs the principal components for all the samples. I am just inputting the .PED and .MAP files in par.PED.EIGENSTRAT. It'd be great if anybody can give me some insight on this. 





convertf plink eigensoft • 1.8k views
ADD COMMENTlink modified 3.1 years ago by Philipp Bayer5.8k • written 3.1 years ago by aritra9020
gravatar for Philipp Bayer
3.1 years ago by
Philipp Bayer5.8k
Philipp Bayer5.8k wrote:

I've ran into this one before - the EIGENSOFT FAQ has it, too:

Question: convertf decides to “ignore” all my samples. Why?
Answer: A likely reason is that you are using a “fam” or “ped” file with a funny value (0, 9 or -9) in column 6. Try setting column 6 to 1.

(Column 6 is the phenotype as far as I remember, and it has no effect on the PCA results)

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Philipp Bayer5.8k

Yes, I saw the same just right after posting :P 

Thanks, Philipp, it works now! 

ADD REPLYlink written 3.1 years ago by aritra9020

Although the answer says that "Try setting column 6 to 1." I assume that it does not influence PCA results at all?

ADD REPLYlink written 8 days ago by Phoenix Mu0

If I remember correctly, that column is reserved for phenotypes, which are not used in the PCA

ADD REPLYlink written 6 days ago by Philipp Bayer5.8k
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