Re:NCI60

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Rajasekhar Moturi

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Aug 4, 2016, 9:48:42 AM8/4/16
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Hi Andrew

 

Greetings of the day!!!

 

I have a small query on NCI60 cell line expression with specific target gene. I downloaded the NCI60 data from your downloads option. I have found there is variation in expression of 1007_s_at (probe) from the file I have downloaded and results displayed online Biogps, not only this specific gene mentioned but all the probes there is a variation from the file downloaded and displayed online. It would be great if you can help on this

 

Thanks in advance

 

 

Regards

Raja moturi

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G Tsueng

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Aug 4, 2016, 2:06:49 PM8/4/16
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Hi Raja,

The NCI-60 file contains the data for two samples for each probe/tissue (demarcated in the data file as '.1' and '.2').
The default display in BioGPS expression viewer/activity chart is an average of the two.

Eg- Interactive chart for the 1007_s_at probe (be sure to check that you are displaying the right probe) gives a value of 43.64 (when hovering over it) for the Huh-7 cells in the NCI-60 dataset
The data csv file gives two values for 1007_s_at for Huh-7: Huh-7.1 = 31.727; Huh-7.2 = 55.551
The average of the two = 43.639

best wishes,
ginger

Rajasekhar Moturi

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Aug 8, 2016, 10:29:40 AM8/8/16
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Hi Ginger

 

Thanks for your kind help. Much appreciated

 

I have two more questions regarding NCI60 cell lines data

 

Ø  Is normalization required for this NCI60 or Is it ok if I consider only raw values given because Human U133A/GNF1H Gene Atlas is normalized with gcmra, so is it necessary to do normalization for NCI60 cell lines expression data

Ø  Can you please send the information on cell lines as NCI60_sample_info.xls (92 KB) only contains information about 56 cell lines rest of them are missing. Ex: huh-7,hek293 cell lines doesn’t contain any information like cell type, tissue type, etc,. in sample_info excel sheet.

 

Thanks in advance!!

 

Regards

Raja

From: Rajasekhar Moturi
Sent: Monday, August 08, 2016 9:40 AM
To: 'G Tsueng'
Subject: RE: NCI60

 

Hi Ginger

 

Thanks a ton for your kind reply with great explanation. Understood

 

Is normalization required for this NCI60 or Is it ok if I consider raw values because Human U133A/GNF1H Gene Atlas is normalized with gcmra.

 

Thanks in advance

 

Regards

Raja

 

 

From: G Tsueng [mailto:gts...@gmail.com]
Sent: Thursday, August 04, 2016 11:37 PM
To: BioGPS
Cc: Rajasekhar

 

Subject: Re: NCI60

G Tsueng

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Aug 8, 2016, 11:50:11 AM8/8/16
to BioGPS, gts...@gmail.com, rajasekh...@gvkbio.com
HI Raja,

-To my knowledge, even the 'raw' or unaveraged values have already been gcmra-normalized.
-Unfortunately, the sheet that's available for download is the best we've got according to the answers in these threads:
 --https://groups.google.com/forum/#!searchin/biogps/NCI60|sort:relevance/biogps/INHCC2Sl5-4/RZydoo5pGrwJ
 --https://groups.google.com/forum/#!searchin/biogps/NCI60|sort:relevance/biogps/wPa2JshTqaM/L__nhdwH2pYJ
 --https://groups.google.com/forum/#!searchin/biogps/NCI60|sort:relevance/biogps/fQuau8q2B9o/JdpTL23iLRkJ

best wishes,
ginger 
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