normalizeByReference package for Affymetrix ChIP-chip data
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@jennifer-judy-3468
Last seen 10.5 years ago
Hello. We are currently trying to apply the normalizeByReference package to Affymetrix ChIP-chip data for human and mouse samples. Specifically, I am looking for advice regarding the background parameters (are control samples sufficient in this case). Additionally, does anyone have advice on how to create a probeAnno object with Affy's bpmap files? Any help is much appreciated! Thanks, Jen
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@wolfgang-huber-3550
Last seen 3 days ago
EMBL European Molecular Biology Laborat…
Dear Jennifer I assume you mean the normalizeByReference function in the tilingArray package. 1. the "background" parameter refers to probes on the array, not samples. Here, you need to specify an (as large as possible) set of probes for which you expect no enrichment signal. These are used to estimate the typical background signal also for all other probes by interpolation. 2. You don't need a probeAnno object to call this function, so I am not sure why you are asking? Please let me know if you have any questions that are not well answered by the manual page of this function. Best wishes Wolfgang ------------------------------------------------ Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber JENNIFER JUDY ha scritto: > Hello. > > We are currently trying to apply the normalizeByReference package to Affymetrix ChIP-chip data for human and mouse samples. Specifically, I am looking for advice regarding the background parameters (are control samples sufficient in this case). Additionally, does anyone have advice on how to create a probeAnno object with Affy's bpmap files? > > Any help is much appreciated! > Thanks, > Jen > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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