ComBat_seq took a very long time

[rongwong1119]

Hi, I was using ComBat_seq for RNA seq data, and I have covar_mod as the argument, which has 8 variables, however, it has been run more than 10 hours, and still not completed, which is wired.

I wonder why it took so long?

[DamienTan]

I have the same issue, have you solved this problem? @rongwong1119

[pyunhyojin5504]

I have the same issue too, in fact I only have 2 covariates but still for over 15 hours, it is in process. It would be really helpful if you share how long it took..! I'm wondering if I have to execute it or not.. Thanks! @rongwong1119 @DamienTan

[rongwong1119]

I now used two covariates, and it took only a few minutes.

On Sat, Apr 2, 2022 at 2:35 AM DamienTan @.***> wrote:

I have the same issue, have you solved this problem?

— Reply to this email directly, view it on GitHub https://github.com/zhangyuqing/ComBat-seq/issues/29#issuecomment-1086565278, or unsubscribe https://github.com/notifications/unsubscribe-auth/APYWYWNEOQLZ3CWV62L43PTVC7TCLANCNFSM5JEJJWBA . You are receiving this because you authored the thread.Message ID: @.***>

[rongwong1119]

I have two covariates, and it took a few minutes.

On Wed, Apr 13, 2022 at 11:58 PM pyunhyojin5504 @.***> wrote:

I have the same issue too, in fact I only have 2 covariates but still for over 15 hours, it is in process. It would be really helpful if you share how long it took..! I'm wondering if I have to execute it or not.. Thanks! @rongwong1119 https://github.com/rongwong1119 @DamienTan https://github.com/DamienTan

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[pyunhyojin5504]

@rongwong1119 Thanks for your quick reply! I'm sure that somethings wrong with my job then... One thing more just in case, I have 1300 samples and 200 genes.. is this matrix size pretty similar to your work? If it is even smaller than your work, I should really abort and check other solutions...!! Thanks again for your quick reply :)

[DamienTan]

I have the same issue too, in fact I only have 2 covariates but still for over 15 hours, it is in process. It would be really helpful if you share how long it took..! I'm wondering if I have to execute it or not.. Thanks! @rongwong1119 @DamienTan

Yep, I used the argument "covar_mod" to add 2 covariates, but it took me more than 4 days and was still running. Finally, I killed this process. Maybe only using the argument "group" can avoid this problem, but there is another problem, which will create some very large values at the adjusted matrix. #20

[rongwong1119]

I have 20000+ genes and 60 samples

On Thu, Apr 14, 2022 at 12:51 AM pyunhyojin5504 @.***> wrote:

@rongwong1119 https://github.com/rongwong1119 Thanks for your quick reply! I'm sure that somethings wrong with my job then... One thing more just in case, I have 1300 samples and 200 genes.. is this matrix size pretty similar to your work? If it is even smaller than your work, I should really abort and check other solutions...!! Thanks again for your quick reply :)

— Reply to this email directly, view it on GitHub https://github.com/zhangyuqing/ComBat-seq/issues/29#issuecomment-1098706744, or unsubscribe https://github.com/notifications/unsubscribe-auth/APYWYWIOP4ATCQUPJKSNA73VE6P4LANCNFSM5JEJJWBA . You are receiving this because you were mentioned.Message ID: @.***>

[maxnest]

Hi all! I faced a similar problem: I have 2 covariates in 'covar_mod' matrix and the analysis has been running for 7 days already. @DamienTan did you manage to solve this problem?

[DamienTan]

Sorry, I didn't solve it! I gave up. @maxnest

[maxnest]

@DamienTan Thanks for the answer. Have you used any other program?

[DamienTan]

@DamienTan Thanks for the answer. Have you used any other program?

@maxnest Haven't! as I commented above, there were another problem using the argument "group". But I didn't use other program.