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PayneLab / cptac

Python packaging for CPTAC data
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CCRCC cancer proteomics data do not have normal tissue type in your latest cptac data #44

Closed zihaoxingstudy1 closed 1 year ago

zihaoxingstudy1 commented 1 year ago

CCRCC cancer proteomics data do not have normal tissue type in your latest cptac data

sabmel commented 1 year ago

Hello! The normal tissue data should be at the bottom of the data frame, appended with a .N. Can you please let us know which proteomics source you were pulling from?

zihaoxingstudy1 commented 1 year ago 
    i pulling the BCM cptac ccrcc proteomics dataset. but it doesn't have normal tissue smaples. it only has 104 tumor samples in your data.

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        Sabrina ***@***.***>

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    9/28/2023 07:30

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          Re: [PayneLab/cptac] CCRCC cancer proteomics data do not have normal tissue type in your latest cptac data (Issue #44)

Hello! The normal tissue data should be at the bottom of the data frame, appended with a .N. Can you please let us know which proteomics source you were pulling from?

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

sabmel commented 1 year ago

Thank you for letting us know! You are right, and that was a mistake on our end. We are working to update the bcm proteomics datasets to include both tumor and normal. I appreciate your patience, and feel free to utilize the 'umich' source until we update the package (it has normal samples).

On Fri, Sep 29, 2023 at 2:14 AM ZihaoXing @.***> wrote:

i pulling the BCM cptac ccrcc proteomics dataset. but it doesn't have normal tissue smaples. it only has 104 tumor samples in your data.

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---- Replied Message ----

From

Sabrina @.***>

Date

9/28/2023 07:30

To

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Cc

@.***> ,

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Subject

Re: [PayneLab/cptac] CCRCC cancer proteomics data do not have normal tissue type in your latest cptac data (Issue #44)

Hello! The normal tissue data should be at the bottom of the data frame, appended with a .N. Can you please let us know which proteomics source you were pulling from?

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/PayneLab/cptac/issues/44#issuecomment-1740491118, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGAFPT47XP6LRSVU57LRQF3X4Z7QFANCNFSM6AAAAAA5E6ZYZU . You are receiving this because you commented.Message ID: @.***>

bm600 commented 1 year ago

Hello @zihaoxingstudy1. We've just updated the package to include all available normal-tissue samples with the Baylor (bcm) source. This is available in v1.5.3. Thanks for bringing this to our attention and thanks for using the package! Let us know if you have any other issues.

zihaoxingstudy1 commented 1 year ago 
    thanks ,i will upgrade the cptac and download the latest  bcm source data

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    10/3/2023 07:31

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     Subject 

          Re: [PayneLab/cptac] CCRCC cancer proteomics data do not have normal tissue type in your latest cptac data (Issue #44)

Hello @zihaoxingstudy1. We've just updated the package to include all available normal-tissue samples with the Baylor (bcm) source. This is available in v1.5.3. Thanks for bringing this to our attention and thanks for using the package! Let us know if you have any other issues.

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zihaoxingstudy1 commented 1 year ago 
    The ucec umich acetylproteomics data are note a suitable data frame format,and there are variable names in the middle of the file.

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        Sabrina ***@***.***>

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    9/30/2023 11:39

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        ,

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     Subject 

          Re: [PayneLab/cptac] CCRCC cancer proteomics data do not have normal tissue type in your latest cptac data (Issue #44)

Thank you for letting us know! You are right, and that was a mistake on our

end. We are working to update the bcm proteomics datasets to include both

tumor and normal. I appreciate your patience, and feel free to utilize the

'umich' source until we update the package (it has normal samples).

On Fri, Sep 29, 2023 at 2:14 AM ZihaoXing @.***> wrote:

i pulling the BCM cptac ccrcc proteomics dataset. but it doesn't have

normal tissue smaples. it only has 104 tumor samples in your data.

@.***

---- Replied Message ----

From

Sabrina @.***>

Date

9/28/2023 07:30

To

@.***>

Cc

@.***>

,

@.***>

Subject

Re: [PayneLab/cptac] CCRCC cancer proteomics data do not have normal

tissue type in your latest cptac data (Issue #44)

Hello! The normal tissue data should be at the bottom of the data frame,

appended with a .N. Can you please let us know which proteomics source you

were pulling from?

—Reply to this email directly, view it on GitHub, or unsubscribe.You are

receiving this because you authored the thread.Message ID: @.***>

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