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tarot0410 / BREMSC

Novel joint clustering method with scRNA-seq and CITE-seq data
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simulated datasets #1

Open sorjuela opened 4 years ago

sorjuela commented 4 years ago

Hi @tarot0410,

Where can I find the code you used to generate the simulated datasets? Or the code for the simulations mentioned in your paper https://academic.oup.com/bioinformatics/article/36/Supplement_1/i542/5870491

Thank you, Stephany

xiangz-108 commented 1 year ago

Why I got this error (shown below) when I applied your method on my real cite-seq data? Thank you. "Error in mem[i, 1] <- which(delta[i, ] == max(delta[i, ])) : replacement has length zero"

tarot0410 commented 1 year ago

Please first check if the following requirements are fulfilled:

  1. Input RNA and protein data are both count matrices (not transformed), each of shape "feature by cell". In other words, the two matrices should be exactly matched by column (i.e., cell barcode).
  2. The input RNA data should have <=1000 features (highly variable genes). The protein data matrix is expected to have dozens to hundreds of features.
  3. For each RNA or protein in the input datasets, there is at least some variability of expression level across all cells. In other words, features with 0 variance (across cells) should be screened out.

If all the conditions above are met, but still the algorithm doesn't run appropriately, then could you share your data with me so that I can take a closer look at it? For confidentiality, you may generate pseudo names for cell barcode and features.

Best, Xinjun

From: xiangz-108 @.> Sent: Friday, April 28, 2023 11:01 AM To: tarot0410/BREMSC @.> Cc: Wang, Xinjun @.>; Mention @.> Subject: Re: [tarot0410/BREMSC] simulated datasets (#1)

Why I got this error (shown below) when I applied your method on my real cite-seq data? Thank you. "Error in mem[i, 1] <- which(delta[i, ] == max(delta[i, ])) : replacement has length zero"

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