Axiom arrays? #1
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Hi @drneavin,
The current VICES implementation only supports Illumina arrays. Can you tell me more about your project and the kind of data you have? It may be possible to code up another solution.
Thanks,
Gregory Zajac
University of Michigan
…Sent from my iPhone
On Feb 11, 2021, at 2:00 AM, drneavin ***@***.***> wrote:
Hello @gjmzajac,
I'm wondering if vices can be used with Axiom array outputs or if it only works on Illumina array outputs?
Thanks!
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Hi @gjmzajac, We have multiple cell lines that have been expanded for biobanking and we want to make sure they are pure populations and have not had any cross-contamination from other lines. Would VICES work if I could generate similar files from the Axiom analysis software? For example, if I could pull the B allele frequency and the allele calls for each individual and then format similar to the example data provided on the wiki site? I'm also wondering if the input should be QC filtered data or if it should be the pre-QC filtered data? Thanks so much for your help! |
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Hi Drew,
Sounds like a cool project. If you can get the data into the right format,
then VICES will be able to analyze it and I would be very curious to know
if it produces reasonable estimates. Pre-QC should be fine. Do you have any
other signs of contamination, like low call rate, excess heterozygosity, or
XXY intensities? Do you have any samples that you know for sure are
contaminated as positive controls?
Be aware, however, that "B Allele Frequency" is NOT the frequency of the B
allele in the population/sample--it is a normalized measure of the probe
intensity based on distance to the centers of the genotype clusters. See
https://www.illumina.com/Documents/products/technotes/technote_cytoanalysis.pdf
for more details.
Thanks,
Greg
…On Thu, Feb 11, 2021 at 9:45 PM drneavin ***@***.***> wrote:
Hi @gjmzajac <https://github.com/gjmzajac>,
We have multiple cell lines that have been expanded for biobanking and we
want to make sure they are pure populations and have not had any
cross-contamination from other lines. Would VICES work if I could generate
similar files from the Axiom analysis software? For example, if I could
pull the B allele frequency and the allele calls for each individual and
then format similar to the example data provided on the wiki site?
I'm also wondering if the input should be QC filtered data or if it should
be the pre-QC filtered data?
Thanks so much for your help!
-Drew
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Hi Greg, I wanted to follow up on this topic and let you know how the results look with Axiom data. I was able to create a file from the Axiom data that has the same structure as the example files. We don't have any other signs of contamination but we are interested in seeing if there are low levels of contamination that may have been missed by the Axiom suite software. Unfortunately we don't have any positive controls with this dataset but we may include one in our next array submission to double check that the data we are getting from Axiom works well in vices. However, with the current data, vices doesn't detect any cross-contamination. However, I receive this error when I run vices on our data: I'm wondering what this implies and if there is something that I should check to alleviate this error? In addition, I wanted to note that two of the software dependencies used by vices either cause errors or are no longer available:
Thanks for your help! -Drew |
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Hi Drew,
Sorry for the late reply. Glad you were able to get it to run! The singular
matrix error comes from attempting to invert (X^T X) as a step for fitting
regression. This can happen if the AFs and the intensities are equal or all
the genotypes are equal, but I have most often gotten it when I have passed
all missing or erroneous data for an individual. Are you able to share the
first 10 lines of the file for this sample?
Using the newer versions of the libraries should not be an issue. Did you
edit the build files to resolve this issue?
Thanks,
Greg
…On Mon, Mar 8, 2021 at 1:16 AM drneavin ***@***.***> wrote:
Hi Greg,
I wanted to follow up on this topic and let you know how the results look
with Axiom data. I was able to create a file from the Axiom data that has
the same structure as the example files. We don't have any other signs of
contamination but we are interested in seeing if there are low levels of
contamination that may have been missed by the Axiom suite software.
Unfortunately we don't have any positive controls with this dataset but we
may include one in our next array submission to double check that the data
we are getting from Axiom works well in vices.
However, with the current data, vices doesn't detect any
cross-contamination. However, I receive this error when I run vices on our
data:
error: matrix singular when regressing sample 67 intensities on AF
I'm wondering what this implies and if there is something that I should
check to alleviate this error?
In addition, I wanted to note that two of the software dependencies used
by vices either cause errors or are no longer available:
- armadillo-8.400.0.tar.xz is no longer available from the sourceforge
address. I ended up using 8.600.1 instead
- libStatGen v1.0.14 caused issues on my system that were reported on
their issue page. I used v1.0.15 instead
Thanks for your help!
-Drew
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Hi Greg, Yes, I just edited the library versions in the build file which worked well. For the singularity error, I get the error for all samples. I've attached the top 20 lines of one of the files - let me know if you can see why the samples may all be returning the singularity error. Thanks again for your help! Cheers, |
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Hi Drew,
Great, can you submit a pull request on Github so I can update the build
files to the current versions of those libraries?
The file you shared with me looks good as far as I can tell without
actually running any tests. Did you get any valid output when you did this?
Are you running this sample together with all 86 others? Were they all
genotyped on the same array, with the same variant list and names? Can you
copy all the standard output you get from the terminal?
Are all the samples from distinct individuals? Relatives should be fine but
I do not think VICES handles duplicates well.
Thanks,
Greg
…On Fri, Mar 12, 2021 at 6:44 PM drneavin ***@***.***> wrote:
Hi Greg,
Yes, I just edited the library versions in the build file which worked
well.
For the singularity error, I get the error for all samples. I've attached
the top 20 lines of one of the files - let me know if you can see why the
samples may all be returning the singularity error.
vice_file_head.txt
<https://github.com/gjmzajac/vices/files/6133671/vice_file_head.txt>
Thanks again for your help!
Cheers,
Drew
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Hi Drew,
To facilitate and speed up your own debugging (which can be slow over
email), the only place this error can be thrown is
https://github.com/gjmzajac/vices/blob/master/src/regression.cpp#L27 here
you can print out the values of each of the variables that go into the
determinant calculation:
nAA
nAB
nBB
sum_AF_AA
sum_AF_AB
sum_AF_BB
sum_AF_sq
And see more of what is going on.
Thanks,
Greg
…On Mon, Mar 15, 2021 at 10:41 PM Gregory Zajac ***@***.***> wrote:
Hi Drew,
Great, can you submit a pull request on Github so I can update the build
files to the current versions of those libraries?
The file you shared with me looks good as far as I can tell without
actually running any tests. Did you get any valid output when you did this?
Are you running this sample together with all 86 others? Were they all
genotyped on the same array, with the same variant list and names? Can you
copy all the standard output you get from the terminal?
Are all the samples from distinct individuals? Relatives should be fine
but I do not think VICES handles duplicates well.
Thanks,
Greg
On Fri, Mar 12, 2021 at 6:44 PM drneavin ***@***.***> wrote:
> Hi Greg,
>
> Yes, I just edited the library versions in the build file which worked
> well.
>
> For the singularity error, I get the error for all samples. I've attached
> the top 20 lines of one of the files - let me know if you can see why the
> samples may all be returning the singularity error.
> vice_file_head.txt
> <https://github.com/gjmzajac/vices/files/6133671/vice_file_head.txt>
>
> Thanks again for your help!
>
> Cheers,
> Drew
>
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> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#1 (comment)>, or
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>
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Hi Greg, Great questions! yes, I can put through a pull request to update the libraries. I'm glad to hear that the file looks good from first glance. I've attached the output from the analysis - all the individuals have nan as the output values: contam_estimates.txt. This is the standard output I get from running vices: Yes, all the individuals were genotyped on the same array on the same plate so the variant names are the same. However, you bring up a good point - some of the individuals have been included twice in this genotype array submission. I just ran vices with unique individuals and got the same error so I don't think that is the reason for this issue. I'll print out all the variables and get back to you about that soon. Thanks! |
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Hi Greg, I figured out why my files were all returning the singular matrix error. The files must be dos files to be effectively parsed by vices. If I run I'll do the pull request today to update the software packages. Thanks for all your help on this issue! And good to know now that vices works on Axiom arrays too. -Drew |
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Hi Drew,
I am really glad to hear you got it to work! The report files I had from
Illumina all had the /r/n line endings so I will try to fix that bug so it
can run with just \n.
Thanks,
Greg
…On Wed, Mar 17, 2021 at 5:43 PM drneavin ***@***.***> wrote:
Hi Greg,
I figured out why my files were all returning the singular matrix error.
The files must be dos files to be effectively parsed by vices. If I run
unix2dos on the files that I generated (which were unix files) before
running vices, the program works well and returns the expected results
without error.
I'll do the pull request today to update the software packages.
Thanks for all your help on this issue! And good to know now that vices
works on Axiom arrays too.
-Drew
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Hello @gjmzajac,
I'm wondering if vices can be used with Axiom array outputs or if it only works on Illumina array outputs?
Thanks!
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