search

wenjie1991 / TSVdb

TCGA Splicing Variation Database Cancer Splicing Variant Database Cancer alternative splicing database
http://www.tsvdb.com
13 stars 3 forks source link

Why do some genes have zero log2 RSEM values #22

Closed hummingbirdbio closed 5 years ago

hummingbirdbio commented 5 years ago

E.g. SCN5A?

wenjie1991 commented 5 years ago

I have checked the SCN5A in Colon cancer and Esophagus cancer datasets. And confirmed that "almost every isoform expression of the gene SCN5A is 0".

By downloading the original data from the "Download Data" link in the top-left of the page, I found the isoform expression values were empty. However, most of the genes did not be affected by this problem. So I suppose the data source from TCGA does not contain the SCN5A isoform expression data.

I do not know if I have solved your problem. Free feel to contact me if you have any question about this tool.

hummingbirdbio commented 5 years ago

Thanks, that's great. I just wanted to make sure it was a TCGA data feature rather than a bug.

Konrad Paszkiewicz, PhD Chief Technology Officer Hummingbird Bioscience Pte. Ltd.

NOTICE: The information contained in this email and any document attached hereto is intended only for the named recipient(s). If you are not the intended recipient, nor the employee or agent responsible for delivering this message in confidence to the intended recipient(s), you are hereby notified that you have received this transmittal in error, and any review, dissemination, distribution or copying of this transmittal or its attachments is strictly prohibited. If you have received this transmittal and/or attachments in error, please notify me immediately by reply e-mail and then delete this message, including any attachments. Thank you for your cooperation.

From: Wenjie Sun notifications@github.com Sent: Sunday, March 10, 2019 5:48:12 AM To: wenjie1991/TSVdb Cc: Konrad Paszkiewicz; Author Subject: Re: [wenjie1991/TSVdb] Why do some genes have zero log2 RSEM values (#22)

CAUTION: This email originated from outside of Hummingbird Bioscience. Do not click links or open attachments from unknown sources.

I have checked the SCN5A in Colon cancer and Esophagus cancer datasets. And confirmed that "almost every isoform expression of the gene SCN5A is 0".

By downloading the original data from the "Download Data" link in the top-left of the page, I found the isoform expression values were empty. However, most of the genes did not be affected by this problem. So I suppose the data source from TCGA does not contain the SCN5A isoform expression data.

I do not know if I have solved your problem. Free feel to contact me if you have any question about this tool.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fwenjie1991%2FTSVdb%2Fissues%2F22%23issuecomment-471249488&data=02%7C01%7Ck.paszkiewicz%40hummingbirdbio.com%7C2be4fb86b1d24172f86808d6a51bfc95%7C3174e1ea58c74d4c8edac8ca1d0ca449%7C0%7C0%7C636877936954119073&sdata=3eoDzdC1RbBCR%2BBEeYnkQ%2B%2ByQLu8sleFzSnQUCHpnkk%3D&reserved=0, or mute the threadhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAs3QdNS7ioLTLX0xn-HwbrPWNTTe7osPks5vVJycgaJpZM4bm1ID&data=02%7C01%7Ck.paszkiewicz%40hummingbirdbio.com%7C2be4fb86b1d24172f86808d6a51bfc95%7C3174e1ea58c74d4c8edac8ca1d0ca449%7C0%7C0%7C636877936954129078&sdata=%2FWt4L7CsL74%2BuNgIuewyadxAfYMNR%2BQvI%2BE4XSBPsHs%3D&reserved=0.