how to deal with multiple probes, control probes and probes with no ENTREX gene identifiers
Dear All,
In microarray analysis, we have the following problems, namely
- Probes that do not have ENTREZ gene identifiers
- Set of probes that map to the same ENTREZ gene id
- Probes that are annotated as Affymetrix control probes, i.e. "AFFX-"
How should we deal with this probe? Is there a paper/book/software addressing this matter? Will the statistics and gene enrichment analysis be affected if you do not remove the above probes.
Thank you
1 answer
I might suggest that you read this paper: Strategies for aggregating gene expression data: The collapseRows R function
Log in to answer this question.
More posts like this
-
How to assess quality of publicly available microarray data
written by Will •
-
How to combine expression values of multiple probes for one gene?
written by bhargavdave1 •
-
Unknown gene names in Clariom D human Gene chip annotation files?
written by mgab •
-
What people do with the probes that doesn't have any GENE SYMBOL in annotation databases?
written by arronar
-
Using limma for Differential Expression test
written by Emilio Marmol
-
Microarray control probes
written by mforde84
-
annotating Agilent Drosophila microarray probes by BLAST
written by yotiao •
-
finding microarray probesets orientation: sense or antisense
written by hosseinkhan •
-
Affymetrix Probe Ids Resolution
written by TitoPullo
-
Microarray: How To Select One Of Multiple Probes Corresponding To A Gene
written by Nasir
