CAMDA Discussion Board

To post messages to the discussion board you must login.

Message Board
View type   
Per page
Total messages: 29     | Prev | Next |
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
 

I summarized this and other information about the CAMDA '06 datasets here:
http://research.stowers-institute.org/efg/2006/CAMDA/index.htm

This answer from the existing FAQ is not correct:

Question: Why are there only 177 subjects
that have microarray data while there are
227 subjects with clinical data.

Answer: Details of the microarray data
acquisition can be found in the microarray
paper in the publications zip file.

After much confusion trying to connect the microarray descriptions in the CAMDA '06 publications to the CAMDA '06 microarray data, I exchanged several E-mails with Suzanne Vernon (sdv), Centers for Disease Control and Prevention:


12/6/2005 E-mail:
efg: "If I'm understanding you correctly (and from what I've observed in the papers), there is no "the microarray paper," and none of the CAMDA papers describe details of the microarray data provided on the CAMDA site."

sdv: "Correct, there is currently no microarray paper from this study/dataset. We are excited and hopeful that CAMDA comes up with some interesting papers/results."

efg comment: The CAMDA '06 publications ZIP contains PDFs of a number of papers that provide background information about Chronic Fatigue Syndrome.

sdv: "but there are none (yet) that have come out with the microarray, genetic, proteomic data" (sdv, 12/4/2005). Some of the information does describe various clinical health assessment surveys.

sdv, 12/1/2005:

"The paper [Whistler, et al, 'Integration of gene expression, ...'] is only provided as background information on the illness and to demonstrate that gene expression profiling of the peripheral blood has utility in describing the heterogeneity of this illness."

"The microarrays we used were from a company called MWG Biotech, the 40K microarray which consists of 2 glass slides (A and B), each with 20,000 features. We provided only gene expression data for the A microarray only. The spreadsheet of csv file have microarrays/samples in columns and features/genes in rows. The data is raw (so [you] can transform, normalize, ...) so there does not seem to be any real good reason to go back to the actual images."

"There are many challenges to this particular dataset; including determining ways to integrate the various types of data to derive new insight into the biology, and new computational approaches for dealing with signal/noise issues in various data types."

sdv, 12/4/2005:

"Each data table has the subjects identified with and ABTID. There were 227 people/subjects eligible for the study. Of these 227 people, only 177 samples from these people gave satisfactory microarray results."

"This is the first study where [we] used the MWG 40K, which was the most recent and comprehensive array. We only used the A slide from this microarray set as the B slide failed all our qc measures. Each subject's blood sample, as identified by ABTID, is hybridized to a microarray slide. This is similar to the Affymetrix approach, one chip:one subject. The detection was not with fluorescence, as Affy uses, but with a resonance light scattering, resulting in a single intensity readout. The microarray slides are imaged with a CCD camera - versus a laser - to generate the tiff images you have on your website. To read more about this approach, see http://www.invitrogen.com/content.cfm?pageid=9912. The image is acquired and intensities quantified using ArrayVision (can also find a link to this software at this site). Once the intensities are captured, we use the csv to import into various analysis tools."

"this data is about as new and fresh to us as it is to you"

efg comment:
Files at MWG Biotech (specifically the Excel file or the TXT file) both have the expected number of probes, 20,160, as found in the CFS microarray datasets, and information identifying the probes.
http://ecom2.mwgdna.com/services/array/download.tcl
http://ecom2.mwgdna.com/download/arrays/arrays/gene_id/txt/gene_id_human_40k_b.txt
http://ecom2.mwgdna.com/download/arrays/arrays/gene_id/xls/gene_id_human_40k_a.xls





 
Send an email to the author of this message Email a copy of this message to a friend  
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
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

© Duke Comprehensive Cancer Center