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Subject File Author Date
Only ~3800 genes but 20,160 probes on Atlas Human 3.8 I Microarray? Earl F. Glynn 29/Nov/2005
Re: GAL files from microarrays images   Patrick McConnell 30/Nov/2005
RE: About Microarray   Patrick McConnell 30/Nov/2005
Re: SNP Data Identification   Patrick McConnell 30/Nov/2005
FAQ is wrong about "the microarray paper": No publication describes actual microarray data to be analyzed   Earl F. Glynn 06/Dec/2005
ArrayVision RLS was used to analze Gene Expression Data   Earl F. Glynn 16/Dec/2005
Proteomic Data: Howto get patient identifiers? Meaning of Spectrum names is not clear.   Peter Bewerunge 28/Dec/2005
 

From existing CAMDA 2006 Data Set FAQ:

Question: Could you please explain the meaning of the spectra names in the H50_Proteinchip Info table and how they relate to patient identifiers?
Answer: The sample name refers to the Subject ID, and each serum sample from each subject is run under all conditions. The spectrum name is the Barcode of the Proteinchip with the well number - this is the unique ID for each spectrum. For example:

Line 738 = 1 080055198 (Bar code) = 29030401 (Subject ID) who is NF (=not fatigued= Sample group) this was run in B (=SpotName : where it was on the ProteinChip) = F1 (Fraction name: sera was frationated F1 to F6) on an H50 chip (=Array type) at a laser reading of 180 (= Laser low)

So, each subject has several readings:

There are 4 chips
There are 6 fractions
There are 2 laser settings (Low and high)
And each sample is done in duplicate.
#################################################################

My Question:
The Bar code 1080055198 exists 16 times with relationship too 8 different patient identifiers (H50_Proteinchip Info table). The directory ".../H50_Low Laser/F1/Bkgd Subtracted" contains the files "1080055198.csv", "1080055198_1.csv", ..., "1080055198_7.csv." How can I map the Bar Code to patient identifiers? Is it like this:

Line 737 = 1080055198 (Bar code /Spectrum name) = 29430602 (Subject ID /Sample name) = A (Spot name) = 1080055198.csv (File Name)

Line 738 = 1080055198 (Bar code /Spectrum name) = 29030401 (Subject ID) = B (Subject ID /Sample name) = 1080055198_1.csv (File Name)

Line 739 = 1080055198 (Bar code /Spectrum name) =28603101 (Subject ID) = C (Subject ID /Sample name) = 1080055198_2.csv (File Name)

Isnīt there an explicit identifier that could be extracted from the SELDI files (e.g. 1080055198.csv) that refers too only one patient ID??

 
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New relevant paper: Chronic Fatigue Syndrome - A clinically empirical approach to its definition and study   Earl F. Glynn 09/Jan/2006
Paper that seems to explain SNP Excel worksheets, COMT, CRHR1, ... TH, TPH2   Earl F. Glynn 18/Jan/2006
No notification when SNP download file was changed on 11/7/2005?   Earl F. Glynn 18/Jan/2006

Last modified on 01/28/2004 10:50:38

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