Progenetix Data Review¶
This is a tracker for datasets which should be reviewed / flagged / re-processed or added to Progenetix in the first place. Please check & comment when done.
- 2022-05-27: PMID:27257180
This mostly looks like noise?
- 2022-04-04 pgx:icdom-84421
The samples are highly skewed towards deletion...
- 2022-02-07 PMID:16737909
- 2022-02-07 PMID:16790082
Excluded due to lacking CNV annotations (source file w/ complex karyotypes but not parsed correctly in FMP).
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2022-02-02 PMID:17934521
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SOLVED 2022-02-02: the 12 samples w/ platform geo:GPL5055 have only chr1 probes; removed. The other 96 arrays (like the exaample below) are GPL5056 and have also genome covering probes
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odd provenance; the samples have been tagged - and seem to correspond - to GSE7428 with the data per sample on the server corresponding to the chr 1 only arrays from GEO
- however, the stored variants & summary profile indicate nice whole-genome CNV profiles
- have to look-up provenance; maybe mix of annotations (from where?) and arrays?
- This example really looks like a combination of whole-chromosome CNVs & array for chr1:
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2022-01-19 PMID:24454681
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noisy
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2022-01-18 geo:GSE58579
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very biased towards deletion
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2022-01-18 PMID:23583283
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noisy and biased to deletion
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2021-12-17 PMID:19330026
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SOLVED 2022-02-03: removed
- only partial genome coverage => should be flagged/removed?
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2021-10-29 PMID:22962301
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baseline shifted towards deletions
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2021-09-07 PMID:23417712
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highly noisy/spiky
- AFAIK was from methylation arrays & kept for DIPG project?
- review / discard / select samples?
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2021-09-07 NCIT:C7431 FIXED
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very strange frequency plot, with just some spikes; looks like either only 2 or such samples with only background are processed (while 3234 are listed), or some value error?
- all (?) child terms are fine
byconeer/frequencymapsCreator.py -d progenetix -p "NCIT:C7431"
doesn't help...