queries about conversion of raw data to log scale

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Mukherjee, Nabanita

Jul 9, 2021, 3:10:45 PMJul 9
to cbiop...@googlegroups.com
My name is Nabanita and I am a novice in the usage of cbioportal and trying to learn how to use the cbioportal in a right way.

I downloaded some data to see the expression of BCL2A1 gene in various cancers. My PI want me to convert the mRNA data in log2 scale and make a graph with that. 
Some of the cancers such as ocular melanoma have very low expression of BCL2A1 and the value is stated as zero. What is the most reasonable way to convert zero to log scale? One of my colleague told me to convert the raw data to log2 scale with the “value+1” method. This can be done by adding +1 to the raw data values and then converting them to log2 values. 

Is this a reasonable way to convert?


Ino de Bruijn

Jul 14, 2021, 12:54:30 PMJul 14
to Mukherjee, Nabanita, cbiop...@googlegroups.com
Hi Nabanita,

Thanks for reaching out!

We don't really provide recommendations on how to process data, but the approach you outlined seems reasonable to me


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Mukherjee, Nabanita

Jul 15, 2021, 9:50:08 AMJul 15
to Ino de Bruijn, cbiop...@googlegroups.com
Thank you so much

From: Ino de Bruijn <i...@ino.pm>
Sent: Wednesday, July 14, 2021 10:54 AM
To: Mukherjee, Nabanita <NABANITA....@CUANSCHUTZ.EDU>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] queries about conversion of raw data to log scale
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