Question: Are Plink MDS plots supposed to complete so quickly?
gravatar for devenvyas
2.7 years ago by
Stony Brook
devenvyas480 wrote:

I ran MDS plots on a data set of >620,000 SNPs and 934 individuals using plink.

I followed the advice of a former labmember as well as this tutorial ( - mainly just the stuff after "To perform MDS analysis in PLINK, we first calculate a file").

plink --file dataset --genome --out dataset
plink --file dataset --read-genome dataset --mds-plot $k --out "dataset_"$k

($k is looped in and is the number of MDS dimensions ranging from 1 to 20).

The first line (genome file creation) does take a while, but I have noticed that the actual mds generation takes about 10 minutes per run and uses about half a gigabyte of RAM, which seems suspiciously quick and non-intensive.

Anyone have any experience with this? (i.e., am I doing something wrong, or is this normal)



mds snp plink • 1.0k views
ADD COMMENTlink written 2.7 years ago by devenvyas480

Actually, once your data has been converted to binary, genome file creation should take less than two minutes with your dataset with PLINK 1.9 on most systems, and --mds-plot should take less than one.

ADD REPLYlink written 2.7 years ago by chrchang5232.9k

This was running on Plink 1.07, single threaded. HPC just got Plink 1.9 installed this morning, so I haven't tried it out yet.

ADD REPLYlink written 2.7 years ago by devenvyas480
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