Would it make sense to remove the probes which have a low p value and bad annotation quality before doing the normalisation (quantile or neqc) across arrays?
•
written
by
dharl •
2 answers
Normalization is done to make the data similar across arrays. Given that all arrays will have unexpressed genes, I doubt that doing so will significantly "improve" results, but I don't have any evidence to support my claim. Filtering is usually applied after normalization (can't think of any large-scale counter-examples) and is probably best based on variance rather than expression levels.
•
written
by
Sean Davis
No, there is no purpose in doing so, and it might make it more difficult for the background correction and normalization algorithms to estimate the background intensity levels. As Sean says, it is much better to whatever filtering you want to do after background correction and normalization steps are completed.
Log in to answer this question.
-
Removing Illumina microarray probes with no expression HumanHT-12v4
written by Bioinformatician •
-
Illumina HumanMethylation - Exclusion Criteria for Poor Quality Samples
written by MoltenLight •
-
Get rid of Low Quality Bases In A Sequence, and which be replaced on removed place?
written by 9521ljh •
-
Minfi probe filtering
written by niutster
-
Microarray Multimapping/Cross-hybridizing probesets
written by Nathaniel •
-
Using pm() function after normalization
written by akutasame •
-
Microarray analysis beadarray with limma gives no differential expression
written by dharl •
-
microRNA microarray filtering
written by mjktfw •
-
Negative B-Statistic Values In Limma/Microarray Differential Expression
written by CrazyB
-
Is It A Good Idea To Trim Rna-Seq Reads Or Just Remove N'S?
written by Rohit
