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BorisovNM / Shambhala2

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Question about the details of dataset P and dataset Q #1

Open Alvis-Jiang opened 1 year ago

Alvis-Jiang commented 1 year ago

Hi, I am a little bit confused about how the dataset P and Q are built, they seem not just simply combined by the RAW data of microarray and RNAseq, could you please guide me how to build the right dataset P and Q from the data on GEO database? Thank you so much.

BorisovNM commented 1 year ago

Dear Dr. Boyu Jang,

Many thanks for your interest in our method.

In fact, you don't need to build your own P- and Q-dataset.

You can use those provided in the Zenodo storehouse.

We achieved he best results with the P0- and Q0-datasets; however, alternative variants, Q1 and P1-P7, are also provided.

Kind regards,

Nicolas

----- Исходное сообщение ----- От: "Boyu Jiang" @.> Кому: "BorisovNM/Shambhala2" @.> Копия: "Subscribed" @.***> Отправленные: Суббота, 28 Январь 2023 г 0:23:19 Тема: [BorisovNM/Shambhala2] Question about the details of dataset P and dataset Q (Issue #1)

Hi, I am a little bit confused about how the dataset P and Q are built, they seem not just simply combined by the RAW data of microarray and RNAseq, could you please guide me how to build the right dataset P and Q from the data on GEO database? Thank you so much.

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Alvis-Jiang commented 1 year ago

Thank you so much for your helpful advice, I also have another question that needs your help, could you tell me what kind of microarray data you use as input data? Are they the raw cel files without any normalization? Or do they need to be normalized to be used as input for Shambhala2? Thank you again.

BorisovNM commented 1 year ago

In fact, you can use the "almost-raw" microarray data, i.e. after the background extraction.

All you need is to convert the CEL files into text format since our code does not work with the CEL format.

----- Исходное сообщение ----- От: "Boyu Jiang" @.> Кому: "BorisovNM/Shambhala2" @.> Копия: "BorisovNM" @.>, "Comment" @.> Отправленные: Суббота, 28 Январь 2023 г 23:37:58 Тема: Re: [BorisovNM/Shambhala2] Question about the details of dataset P and dataset Q (Issue #1)

Thank you so much for your helpful advice, I also have another question that needs your help, could you tell me what kind of microarray data you use as input data? Are they the raw cel files without any normalization? Or do they need to be normalized to be used as input for Shambhala2? Thank you again.

-- Reply to this email directly or view it on GitHub: https://github.com/BorisovNM/Shambhala2/issues/1#issuecomment-1407481183 You are receiving this because you commented.

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Alvis-Jiang commented 1 year ago

Got it. Thank you very much for your help, now I have a better understanding of Shambhala2. It is more powerful and efficient than I thought!