User: Gurkenkönig

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Posts by Gurkenkönig

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When to Correct for Cell Type Heterogeneity in ChAMP Pipeline
... When is the right time to correct for different cell counts in whole blood samples on Illumina EPIC Chips when analysing the data with the ChAMP-Pipeline? After Normalization or after Batch Effect Correction? And is the method even working with EPIC data? ...
microarray written 8 weeks ago by Gurkenkönig0
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ChAMP champ.norm BMIQ produces differing results
... The method produces different results with each run. Can anyone give me a hint on how to fix this behavior? set.seed(42) library("ChAMP") myLoad_test1 <- champ.load(directory = "data/raw/iDat_t0", method="ChAMP", methValue="B", autoimpute= ...
microarray normalization written 8 weeks ago by Gurkenkönig0
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champ.runCombat is failing: "invalid 'row.names' length"
... I have read in an existing matrix of 450K beta values with champ.filter and linked it to a dataframe of covariates. So far everything worked perfectly (champ.QC, champ.norm, champ.SVD) only in champ.runCombat I always get the same error message. [===========================] [<< CHAMP.RUNCOM ...
champ written 8 months ago by Gurkenkönig0
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Repeated measurements wtih limma
... I have EPIC array methylation data and would like to check for differential methylation. +------+-----+ | time | id | +------+-----+ | t0 | P1 | +------+-----+ | t1 | P1 | +------+-----+ | t0 | P2 | +------+-----+ | t1 | P2 | +------+-----+ | ... | ... | +------+-----+ So far I have al ...
limma limma design matrix written 9 months ago by Gurkenkönig0 • updated 9 months ago by Aaron Lun23k

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