Re:NCI60
Rajasekhar Moturi
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
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
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
-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