CCRCC cancer proteomics data do not have normal tissue type in your latest cptac data
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zihaoxingstudy1 commented
CCRCC cancer proteomics data do not have normal tissue type in your latest cptac data
sabmel commented
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
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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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?
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sabmel commented
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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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?
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bm600 commented
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
thanks ,i will upgrade the cptac and download the latest bcm source data
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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 @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
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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Date
9/30/2023 11:39
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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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