Inconstancy in the downloaded study table

[Shelly Aviv]

Hello,

I have downloaded a study data using the R library cbioportalR.

For some reason, I found inconsistency between the file I’ve downloaded using the R library and the one I’ve downloaded from the web portal.

For example, looking at copy number alteration table, for the study Id acc_tcga_pan_can_atlas_2018, I looked for the value of gene A1BG for sample id TCGA-OR-A5J1-01.

This is the R code that I’ve used:

df <- get_genetics_by_study(study_id = "acc_tcga_pan_can_atlas_2018")

cna_A1BG <- subset(df$cna, hugoGeneSymbol == "A1BG" & sampleId == "TCGA-OR-A5J1-01")

dim(cna_A1BG)

[1] 0 9

There is no such entry in the downloaded table, but in the web portal there is, and the alteration value is -1:

acc_tcga_pan_can_atlas_2018

TCGA-OR-A5J1-01

-1

Moreover, when I looked at the unique values of “alteration” column it has only either 2 or -2.

Just to make sure, is this the right way to interpret the alteration values:

-2 = homozygous deletion; 

-1 = hemizygous deletion; 

0 = neutral / no change; 1 = gain; 

2 = high level amplification.

 

 

I would really appreciate your help on that,

Thanks,

Shelly

 

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[Benjamin Gross]

Hi Shelly,

I’m not finding an alteration for this gene/sample combination (see image below and CNA table w/filter for A1BG). Can you send me a link to the web portal where you see this alteration value?

You are correctly interpreting the CNA discrete values.  Here is further info on our FAQ

https://docs.cbioportal.org/user-guide/faq/#what-do-amplification-gain-deep-deletion-shallow-deletion-and--2--1-0-1-and-2-mean-in-the-copy-number-data

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[Shelly Aviv]

Hi Benjamin,

 

Thank you for the fast reply!

The steps I did are as follow:

1. Type A1BG in the query line
2. Go to Download tab
3. Download Copy-number Alterations (OQL is not in effect)

 

The downloaded file is attached, and the example I gave is in line 202.

Again, from the file I’ve downloaded using the R api, the only alteration values are -2 and 2 for this study id.

 

 

Thanks again for the help!

 

From: Benjamin Gross <benjami...@gmail.com>
Date: Tuesday, 11 July 2023 at 18:51
To: Shelly Aviv <shelly...@gsk.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>, Eyal Itskovits <eyal.x.i...@gsk.com>
Subject: Re: [cbioportal] Inconstancy in the downloaded study table

EXTERNAL

[Benjamin Gross]

Hi Shelly,

I was able to confirm what you see.  This is independent of the use of the R library.  No alteration found on web pages, but alteration found in downloaded cna file.  I’ve submitted an issue to the dev team to take a closer look.  Here is the link to track progress:

https://github.com/cBioPortal/cbioportal/issues/10266

Best,

Benjamin

On Jul 11, 2023, at 2:48 PM, Shelly Aviv <shelly...@gsk.com> wrote:

Hi Benjamin,

 

Thank you for the fast reply!

The steps I did are as follow:

1. Type A1BG in the query line
2. Go to Download tab
3. Download Copy-number Alterations (OQL is not in effect)

 

The downloaded file is attached, and the example I gave is in line 202.

Again, from the file I’ve downloaded using the R api, the only alteration values are -2 and 2 for this study id.

 

 

Thanks again for the help!

 

From: Benjamin Gross <benjami...@gmail.com>
Date: Tuesday, 11 July 2023 at 18:51
To: Shelly Aviv <shelly...@gsk.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>, Eyal Itskovits <eyal.x.i...@gsk.com>
Subject: Re: [cbioportal] Inconstancy in the downloaded study table

EXTERNAL

Hi Shelly, 

 

I’m not finding an alteration for this gene/sample combination (see image below and CNA table w/filter for A1BG). Can you send me a link to the web portal where you see this alteration value?

 

You are correctly interpreting the CNA discrete values.  Here is further info on our FAQ

https://docs.cbioportal.org/user-guide/faq/#what-do-amplification-gain-deep-deletion-shallow-deletion-and--2--1-0-1-and-2-mean-in-the-copy-number-data

 

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<cna_A1BG.csv>