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Question about the cpp code #2

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Tsukumo1 opened this issue Dec 12, 2022 · 9 comments
Open

Question about the cpp code #2

Tsukumo1 opened this issue Dec 12, 2022 · 9 comments

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@Tsukumo1
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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?

@noirritchandra
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noirritchandra commented Dec 14, 2022 via email

@Tsukumo1
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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?

@noirritchandra
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noirritchandra commented Jan 12, 2023 via email

@noirritchandra
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noirritchandra commented Jan 12, 2023 via email

@Tsukumo1
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Hi for PART 6 of your paper, Cells with low read counts are discarded, as we lack reliable gene expression measurements for these cells, and data are normalized following Lun et al.(2016). We remove non-informative genes using M3Drop (Andrews and Hemberg,2018).. I tried the method you mentioned, but I want to know exactly how you got a final dataset with n = 531 cells and p = 7,666 genes. Thank u for your reply!

@Tsukumo1
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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!

@noirritchandra
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noirritchandra commented Jan 30, 2023 via email

@Tsukumo1
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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?

@noirritchandra
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noirritchandra commented Jan 31, 2023 via email

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