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Question about the cpp code #2
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Thanks for your interest in my work. In my compiler, DOUBLE_EPS works fine
but this is an issue people complained about before. Can you try replacing
the DOUBLE_EPS by datum::eps? datum::eps is in the Armadillo library:
[image: image.png]
Let me know if this works.
Best,
Noirrit
…On Mon, 12 Dec 2022 at 21:13, Tsukumo1 ***@***.***> wrote:
hi thank u for your sharing! I have a little question about the cpp code.
When I try to run the rmarkdown, it shows something wrong in the cpp file
line 436, DOUBLE_EPS was not declared.
may I check what is "DOUBLE_EPS" refer to?
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Hi! Thank you very much for your reply. That's working! I have another question about the cpp code, why don't you return parameters in the DL_mixture? Which variables are used to represent parameters......and I also want to ask about the data preprocessing method you used in PART 6 of your paper. Sorry for all the questions... ! But if it is convenient, could you also provide the code in the paper? |
*Hi! Thank you very much for your reply. That's working! I have another
question about the cpp code, why don't you return parameters in the
DL_mixture? Which variables are used to represent parameters...... - * Since
our primary interest is in clustering high-dimensional data, we are only
returning the cluster allocation variables acrosss MCMC samples. The
residual error variance parameters σj2's and the factor loading matrix Λ
are the only parameters you can return; it would be a simple change in the
return statement in the DL_mixture function.
You can also consider the mixture parameters [image: \mu_{i}]'s and [image:
\Delta_{i}]'s in eqn (8) of the arxived paper as parameters but due to
label switching those are not identifiable. Hence we are not returning
these parameters.
*and I also want to ask about the data preprocessing method you used in
PART 6 of your paper.*- Let me know your questions, I'll try my best to
answer those.
*Sorry for all the questions... ! But if it is convenient, could you also
provide the code in the paper?*- We do not have plans for that since the
codes are available on Github.
I hope this helps.
Best
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*Hi! Thank you very much for your reply. That's working! I have another
question about the cpp code, why don't you return parameters in the
DL_mixture? Which variables are used to represent parameters...... - * Since
our primary interest is in clustering high-dimensional data, we are only
returning the cluster allocation variables acrosss MCMC samples. The
residual error variance parameters σj2's and the factor loading matrix Λ are
the only parameters you can return; it would be a simple change in the
return statement in the DL_mixture function.
You can also consider the mixture parameters [image: \mu_{i}]'s and [image:
\Delta_{i}]'s in eqn (8) of the arxived paper as parameters but due to
label switching those are not identifiable. Hence we are not returning
these parameters.
*and I also want to ask about the data preprocessing method you used in
PART 6 of your paper.*- Let me know your questions, I'll try my best to
answer those.
*Sorry for all the questions... ! But if it is convenient, could you also
provide the code in the paper?*- We do not have plans for that since the
codes are available on Github.
I hope this helps.
Best
Noirrit
…On Tue, 10 Jan 2023 at 02:24, Tsukumo1 ***@***.***> wrote:
Hi! Thank you very much for your reply. That's working! I have another
question about the cpp code, why don't you return parameters in the
DL_mixture? Which variables are used to represent parameters......and I
also want to ask about the data preprocessing method you used in PART 6 of
your paper.
Sorry for all the questions... ! But if it is convenient, could you also
provide the code in the paper?
—
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<#2 (comment)>,
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Hi for PART 6 of your paper, |
Hi I also want to check if you choose TMM or DESeq to normalize the data? I got a bad cluster by using both of them. So I want to confirm what's wrong with it. Looking for your reply! |
Hi,
I apologize for not responding to your earlier email. I can not really
provide you with the exact script; I was part of a bioinformatics lab where
I used their scripts to preprocess the data. However, I do not have access
to those anymore.
Since the data is really high-dimensional with not that many cells, I
discarded those genes with <30% observed counts across all cells.
I hope this helps.
Best,
Noirrit
…On Mon, 30 Jan 2023 at 04:22, Tsukumo1 ***@***.***> wrote:
Hi I also want to check if you choose TMM or DESeq to normalize the data?
I got a bad cluster by using both of them. So I want to confirm what's
wrong with it. Looking for your reply!
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Thank u for your reply! I'll try then. And another question, did u modify the parameters in LAMB when dealing with the real data? |
No, I did not. Those are exactly the same as suggested in the manuscript.
Noirrit
…On Mon, 30 Jan 2023 at 19:27, Tsukumo1 ***@***.***> wrote:
Thank u for your reply! I'll try then. And another question, did u modify
the parameters in LAMB when dealing with the real data?
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hi thank u for your sharing! I have a little question about the cpp code. When I try to run the rmarkdown, it shows something wrong in the cpp file line 436, DOUBLE_EPS was not declared.
may I check what is "DOUBLE_EPS" refer to?
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