Comments (7)
goldenflaw
commented on August 17, 2024
Hi Bosh,
Are you sure? I'm not looking at this now, but could you make sure that
this bugfix is incorrect?
Yang
On Nov 3, 2017 7:14 PM, "Boxiang Liu" <[email protected]> wrote:
HI @davidaknowles <https://github.com/davidaknowles>,
The PCA output from prepare_phenotype_table.py has N columns, where N is
the number of clusters. Instead, I think one wants M columns, where M is
the number of individuals. On line 149 there is matrix =
np.transpose(matrix) # important bug fix, which seems to be causing the
problem.
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boxiangliu
commented on August 17, 2024
@goldenflaw Unless there is a version difference in sklearn, I am quite sure. Here is an example input. Maybe try to see if you can reproduce on your machine.
sqtl_perind_numers.counts.gz
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davidaknowles
commented on August 17, 2024
Yeah I think you're right about this Bosh: on the example_data the PCs matrix I get is nPCs x 1605 (1605=num of quantifiable introns), whereas it should be nPCs x 10 (number of samples). Removing that transpose line gets the correct dimension. Is this the right way around for fastQTL or should it be |samples| x |PCs| ?
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goldenflaw
commented on August 17, 2024
Interesting, someone else reported that bugfix, and I swore they were right.
…On Sun, Nov 5, 2017 at 12:03 AM, David A. Knowles ***@***.***> wrote:
Yeah I think you're right about this Bosh: on the example_data the PCs
matrix I get is nPCs x 1605 (1605=num of quantifiable introns), whereas it
should be nPCs x 10 (number of samples). Removing that transpose line gets
the correct dimension. Is this the right way around for fastQTL or should
it be |samples| x |PCs| ?
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xtmgah
commented on August 17, 2024
Hello @boxiangliu @davidaknowles @goldenflaw
I have the same issue, So,should I simply remove this line: " matrix = np.transpose(matrix) # important bug fix" ?? I am confused. Thanks.
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xtmgah
commented on August 17, 2024
And which is the final value for PCA calculation? can we reproduce the PCA from "perind.counts.gz.qqnorm_chr.all"?
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goldenflaw
commented on August 17, 2024
The bug fix has been reverted. Sorry for the delay!
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