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natsuhiko / rasqual

Robust Allele Specific Quantification and quality controL
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Different output on example run when sample size is increased by 1 #23

Closed liangyy closed 5 years ago

liangyy commented 5 years ago

Hi Natsuhiko,

I am getting familiar with RASQUAL right now and testing the example run. If I increase the sample size from 24 to 25, the top SNP changes. Does it have something to do with setting prior or some internal parameters? So that I should always set the exact number of samples rather than giving rasqual a rough estimate of the minimum like -m and -l?

$ tabix data/chr11.gz 11:2315000-2340000 | rasqual -y data/Y.bin -k data/K.bin -n 24 -j 1 -l 378 -m 600     -s 2316875,2320655,2321750,2321914,2324112 -e 2319151,2320937,2321843,2323290,2324279     --fix-genotype -t
1   rs2521269   11  2321095 C   A   0.604167    0.041818    0.965100    -13.4603461799  66.1521580593   0.092827    0.000033    0.525289    2.934533    4.180899    11  83  7   4   2321095 -197.774783 0   0.995314    0.993467
$ tabix data/chr11.gz 11:2315000-2340000 | rasqual -y data/Y.bin -k data/K.bin -n 25 -j 1 -l 378 -m 600     -s 2316875,2320655,2321750,2321914,2324112 -e 2319151,2320937,2321843,2323290,2324279     --fix-genotype -t
1   rs12224967  11  2321284 G   A   0.340000    0.978724    0.978100    -11.0378792353  55.5774037017   0.887923    0.000037    0.494012    1.963603    4.263620    11  102 7   4   2321284 -201.188234 0   0.995295    0.992414

If I further increase the sample size, I got an error or some output like

$ tabix data/chr11.gz 11:2315000-2340000 | rasqual -y data/Y.bin -k data/K.bin -n 100 -j 1 -l 378 -m 600     -s 2316875,2320655,2321750,2321914,2324112 -e 2319151,2320937,2321843,2323290,2324279     --fix-genotype -t
gsl: gamma.c:1180: ERROR: error
Default GSL error handler invoked.
Aborted
$ tabix data/chr11.gz 11:2315000-2340000 | rasqual -y data/Y.bin -k data/K.bin -n 200 -j 1 -l 378 -m 600     -s 2316875,2320655,2321750,2321914,2324112 -e 2319151,2320937,2321843,2323290,2324279     --fix-genotype -t
1   SKIPPED 11  -1  N   N   -1.0    -1.0    -1.0    0.0 0.0 -1.0    -1.0    -1.0    -1.0    -1.0    0   0   -1  -1  -1  0.0 0   -1.0    -1.0

Are they expected?

Thanks!

Yanyu

natsuhiko commented 5 years ago

Hi Yanyu,

I don't imagine any situation in which you only know the lower bound of the sample size for QTL mapping. We know that the test data is composed of the 24 samples, because we collected the 24 samples.

Best regards, Natsuhiko

liangyy commented 5 years ago

Hi Natsuhiko,

Thank you for the explanation! Got your point. I will close this issue.

Yanyu