diff options
Diffstat (limited to 'topics/systems/mariadb/ProbeData.gmi')
| -rw-r--r-- | topics/systems/mariadb/ProbeData.gmi | 48 |
1 files changed, 0 insertions, 48 deletions
diff --git a/topics/systems/mariadb/ProbeData.gmi b/topics/systems/mariadb/ProbeData.gmi deleted file mode 100644 index c339571..0000000 --- a/topics/systems/mariadb/ProbeData.gmi +++ /dev/null @@ -1,48 +0,0 @@ -# ProbeData - -## Tags - -* assigned: pjotrp, aruni -* status: unclear -* priority: medium -* type: enhancement -* keywords: database, mariadb, innodb, ProbeData - -## Description - -Probe level data is used to examine the correlation structure among the -N probes that have the same nominal target. Sometimes several probes -are badly behaved or contain SNPs or indels. -The well-behaved probes were then be used in GN1, at the user's -discretion, to make an eigengene that sometimes performs quite a bit -better than the Affymetrix probeset. Essentially, the user could design -their own probesets. And the probe level data is quite fascinating to -dissect some types of cis-eQTLs—the COMT story I have attached is a -good example. Here is figure 1 that exploits this unique feature: - -Ideally, the probe level data would be in GN2 with the same basic -functions as in GN1. - -All we need in GN2/3 is a new table to display the probe level -expression (mean) with their metadata (melting temperature, sequence, -location, etc). The probeset ID is the Table header and name (the -parent), and the probes in the table are the children. Using our now -standard DataTable format should work well. -We have a similar parent-child relation among traits with peptides and -proteins. All of the peptides of a single protein are should have -the same parent probeset/protein. And peptides could be entered as -"probes" in the same way that we did for Affymetrix. - -Arun—I wonder whether this hierarchy could be usefully combined to -handle time-series data. Probably not ;-) -In the case of probes and probesets there is almost never any overlap -of probe sequence—all are disjoint. That is also usually true of -peptides and proteins. - -Pjotr, the reason we have not added much probe level data to GN1 or GN2 -is because we did not have the bandwidth. Arthur simply did not have -time and I did not push the issue. Instead we just started loading the -probe level data separately as if they were probesets. This is what we -have done for peptide data and the reason that there are now "parallel" -data sets—one labeled "protein" and another as "peptide" or as "gene -level" and "exon level". We just collapse the hierarchy. |