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License: MIT License
NOWAC data cleaning package
License: MIT License
lumiHumanIDMapping
increase it to 2 or something
Change to Mutual information: [number w 3 significant digits]
something like install_preprocessing()
that does installs everything in suggested_packages
from bioconductor
This message re filtering out probes:
Filtered out 3417 probes.
Should maybe say why (aggregating across probes that map the same gene)
In preprocessing it would be nice to get an auto-generated bit of text that explains the process for use in papers and reports. Something like:
A probe must detect a signal with p-value <= [something] in at least [some fraction] of the samples. Removed [n1] probes that didn’t fulfill this. Removed an additional [n2] probes with bad annotation quality, finally filtered out [n3] probes by aggregating across probes that detect the same gene. This leaves [n] genes.
[ + more text here about background correction and normalization]
This is a lot faster than the built-in loess()
This message:
Removing 32748 probes that were not present in at least 25 % of the samples.
Should also take into acct that this is at a certain detection p-value threshold.
rewrite what the prob
parameter does
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