I would like to use the PowerMarker software to analyze my molecular marker data but when I am following the tutorial I find an error at the end of it trying to compute the summary statistics.
My database is a binary matrix of 0 and 1 and ? when I have missing data. I have a total number of individuals for my group of markers. Each marker have a different number of alleles and I think that's when the program fails me. I understand that only one allele works for haplotype format and two for the genotype format. How can I solve this problem? I think my error is in the original database.
Example of part of my database: 5 samples that mean 5 individuals analized and 2 markers (Marker-1 with 3 alleles and Marker-2 with 2 alleles):
Samples Marker-1 Marker-1 Marker-1 Marker-2 Marker-2
Sample 1 1 0 1 ? 0
Sample 2 ? 0 0 1 0
Sample 3 1 1 0 0 1
Sample 4 0 ? 1 1 ?
Sample 5 1 1 0 0 1
I used to use PowerMarker a lot but sadly I can’t get it to work on my 64 bit laptop so I’ve given up on it. It’s a shame it is no longer maintained.
Looking at your example file, I think PowerMarker, at least as I used to read in the data will interpret the columns as chromosomes rather than alleles. So the first marker appears to be bi-allelic but in a triploid and the second marker bi-allelic in a diploid. I would try coding the separate alleles as 1, 2...n or similar and have two columns per marker. I would also be wary of spaces in the sample names: use “sample_1” rather than “sample 1”.
Ian,
Thank you very much for your interest and advice!
I have tried to consider each allele as an independent marker with the haplotype analysis but neither solve the problem. I will try to put the alleles in groups of two to see if the error occurs.
Thank you very much again!
Rocío,
Ian's comment about spaces in filenames is important. Because these are all using command-line tools, spaces, periods, and sometimes hyphens can stall the process. Also in areas were you have missing data, frequently NA is used instead of a question mark. I recall seeing some programs use "-999". If I didn't have a test to write - I'd look for that for you :-)
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