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Ginsparg did agree, however, to share arXiv's flagging data with ScienceInsider.
"This allows the scientific community to flag data and problems when they are there," he said.
Clones that consistently behaved poorly (e.g., flagged data in >20% of arrays) were identified and excluded from all analyses.
Flag data from the MAS5 analysis was used to derive a probeset list where at least 19 out of 25 samples had a present or marginal call.
The orientation of reads was calculated from the SAM bit flag data.
Correspondingly, XIAP (D242E -Flag appeareD242E -Flage potent in inhibiting appeareds compared wito WT-XIAP-Flag (data not shown).
Instead, we established an algorithm designed to flag data that are selected for a partial test-retest procedure.
Incomplete or incorrectly entered case report forms (CRFs) were returned to study nurses for revision of missing or flagged data.
The DCC data manager also conducted a careful review, and incomplete or incorrectly entered CRFs were returned to the study physician coordinators, who reviewed the missed or flagged data with the co-investigators and study nurses.
Moreover, CEL files were analyzed using the Affymetrix MAS 5.0 algorithm to obtain the flag data, which have been used to filter the Robust Multi-array Average-normalized data.
The intent was to acquaint the students with this widely used software and to present some of the important low-level analysis such as normalization and quality control involving preprocessing and flagging data as well as advanced methodology (pathway analysis).
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