Limma and EMPTY gene id for specific blocks of rows
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Ng Stanley ▴ 230
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Last seen 10.2 years ago
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Yannick Wurm ▴ 220
@yannick-wurm-2314
Last seen 10.2 years ago
Hi Stanley, you'll probably want to do something along these lines: >spotTypes <- readSpotTypes() which requires that a SpotType.txt file in the current directory. Contents of the file look like this: SpotType ID Color Gene * black Spikein alien* red Blank EMPTY yellow Then before fitting, you can do something like this: >isGene = MA.p$genes$Status=="Gene" >fit = lmFit(MA.p[isGene,], design) Kind regards, yannick -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html On Mar 11, 2008, at 8:43 , Ng Stanley wrote: > Hi, > > I am using limma package to process some gpr files, which contained > EMPTY > gene id for specific blocks of rows. Couple of questions > A) Before what stage should these "EMPTY" rows be deleted. I used > functions: > backgroundCorrect, normalizeWithinArrays, lmFit, contrasts.fit, > eBayes ? > B) In relation to A), are there any functions in limma that I can > invoke to > delete those "EMPTY" rows ? > C) What are those "EMPTY" rows ? > > Thanks > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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Wei Xu ▴ 100
@wei-xu-2693
Last seen 10.2 years ago
Hi, all, I have question about the within-array replicates analysis with limma. The replicates for each spot in my cDNA microarray are irregular- spaced. There are 3 replicates for each spot, which are randomly distributed in the array. When I entitled "irregular=True, ndup=3, spacing=1", I thought the space will be counted automatically based on gene IDs. However, in the output table, I can still find some genes listed twice with different values (i.e. B values, p-values, etc). Did I do anything wrong with that? I went through lots of examples online, and most samples with replicated spots are regulated spaced. Could you please tell me what I am supposed to do with this kind of problem? I really appreciate it. Thanks. Wei
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