there are 6 text files containing summary gene expression data from illumina 6 x 2 human gene expression arrays. the files are: 1. ceuc
There are 6 text files containing summary gene expression data from
illumina 6 x 2 Human gene expression arrays.
The files are:
1. CEUc_120_gene_profile.txt
30 CEPH HapMap children
30 individuals x 2 IVTs x 2 replicate hybridizations/IVT = 120 hybs
2. CEUp_240_gene_profile.txt
60 CEPH HapMap unrelated parents
60 individuals x 2 IVTs x 2 replicate hybridizations/IVT = 240 hybs
3. CHB_180_gene_profile.txt
45 CHB HapMap unrelated adults
45 individuals x 2 IVTs x 2 replicate hybridizations/IVT = 180 hybs
4. JPT_180_gene_profile.txt
45 JPT HapMap unrelated adults
45 individuals x 2 IVTs x 2 replicate hybridizations/IVT = 180 hybs
5. YRIc_120_gene_profile.txt
30 YRI HapMap children
30 individuals x 2 IVTs x 2 replicate hybridizations/IVT = 120 hybs
6. YRIp_240_gene_profile.txt
60 YRI HapMap unrelated parents
60 individuals x 2 IVTs x 2 replicate hybridizations/IVT = 240 hybs
Each file contains 7 lines of text before the start of the data. These
lines contain information output from BeadStudio about the date the
file was made, normalization method, etc. These lines can be ignored.
The data is arranged in 6 tab-delimited columns as output by
BeadStudio with no normalization.
The column headings are:
GroupID: This is a unique identifier for a single hybridization to a
chip.
The identifier contains information about the person (by NA number),
the IVT and the replicate (of the IVT).
The form is NA#_IVT#_replicate#, e.g. NA18951_1_2
Each individual has 4 replicates in total (2 IVTs and 2 hybs/IVT).
TargetID: This is basically equivalent to the probeID. For the whole
genome arrays, BeadStudio no longer outputs a numerical probeID
identifier. Each TargetID is unique (there are 47,293 targets output
for each hybridization).
AVG_Signal: Average intensity across all beads of a single TargetID.
BEAD_STDEV: Standard deviation of intensity values across all beads of
a single Target ID.
Avg_NBEADS: Number of beads of a single TargetID.
Detection: probability of detection of a single TargetID.