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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
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STEP 9. ERROR input matrix of obj1 and obj2 do not match #79

Closed yasserIRCM closed 5 years ago

yasserIRCM commented 5 years ago

Hi there.

I need some insight into this function that I don't understand completely (I am trying to be generous with my brain today, because frankly speaking I didn't understand it at all)

Error in runDiffusionMapsExtension(obj1 = x.landmark.sp, obj2 = x.query.sp, : dimentions of input matrix of obj1 and obj2 do not match

x.landmark.sp number of barcodes: 5999 number of bins: 479013 number of genes: 0 number of peaks: 0 number of motifs: 0 x.query.sp number of barcodes: 2894 number of bins: 479013 number of genes: 0 number of peaks: 0 number of motifs: 0

so afterwards I tested with exactly half my barcodes 4447 and it worked only if we didn't filter out cells of bin coverage less than 1,000 (because if we do, we end up with landmark=4446 and x.query.sp=4447, which stop the pipeline from progressing)

is there any downside to reducing our size from 8894 to this number 4447? does it that our sample size has been halved? also does it reduce the robustness of the statistical testing needed afterwards.

thanks a lot regards.

r3fang commented 5 years ago

Hi there,

This is clearly a bug, I will fix it today. I just updated this tutorial two days ago, it is still ongoing process. The sampling-extension is for a large dataset that has over 10,000 cells, in your case, I don’t think you need to perform sampling-extension. Instead, you can treat your x.sp just as the landmarks.

-- Rongxin Fang, Ren Lab Ludwig Cancer Research Bioinformatics Ph.D. Student University of California, San Diego

On Aug 29, 2019, at 8:45 AM, yasserIRCM notifications@github.com wrote:

Hi there.

I need some insight into this function that I don't understand completely (I am trying to be generous with my brain today, because frankly speaking I didn't understand it at all)

Error in runDiffusionMapsExtension(obj1 = x.landmark.sp, obj2 = x.query.sp, : dimentions of input matrix of obj1 and obj2 do not match

x.landmark.sp number of barcodes: 5999 number of bins: 479013 number of genes: 0 number of peaks: 0 number of motifs: 0 x.query.sp number of barcodes: 2894 number of bins: 479013 number of genes: 0 number of peaks: 0 number of motifs: 0

so afterwards I tested with exactly half my barcodes 4447 and it worked only if we didn't filter out cells of bin coverage less than 1,000 (because if we do, we end up with landmark=4446 and x.query.sp=4447, which stop the pipeline from progressing)

is there any downside to reducing our size from 8894 to this number 4447? does it that our sample size has been halved? also does it reduce the robustness of the statistical testing needed afterwards.

thanks a lot regards.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/79?email_source=notifications&email_token=ABT6GGZ7LJTH6G3FB3KEHITQG7VILA5CNFSM4ISD4ZH2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HIHUGZA, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG6V34U64SDIIUEXCKDQG7VILANCNFSM4ISD4ZHQ.

yasserIRCM commented 5 years ago

Hi there

could you please tell how to use the x.sp directly. because I skipped the sampling step 4 as well as step 9. but when we can't plot anything. it returns that the dimensional reduction isn't complete.

could you tell me what I missed.

thanks a lot

r3fang commented 5 years ago

can you check the first example in the GitHub which does not require sampling. Also, you need to update the package to the latest version.

-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On Aug 30, 2019, at 5:45 PM, yasserIRCM notifications@github.com wrote:

Hi there

could you please tell how to use the x.sp directly. because I skipped the sampling step 4 as well as step 9. but when we can't plot anything. it returns that the dimensional reduction isn't complete.

could you tell me what I missed.

thanks a lot

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/79?email_source=notifications&email_token=ABT6GG7AD6FYW2GEM3IBUV3QHG5JTA5CNFSM4ISD4ZH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5TBYZQ#issuecomment-526785638, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG4IP3IRM7DRYSZO443QHG5JTANCNFSM4ISD4ZHQ.