[BioC] arrayQualityMetrics error with MAList

[Daniel Aaen Hansen]

Dear Wolfgang,

I just tested arrayQualityMetrics 3.11.4 on 'MAList' objects and it is working for me (it generates a report). However, I am not sure I understand what is going on. From the box plot and density plot it looks like it is using data that are not log transformed as some expression values are very large. Surprisingly, it makes no difference whether I set 'do.logtransform=FALSE' or 'do.logtransform=TRUE'. The plots are identical and looks as if they are made on non-log-transformed data.

I also tried to convert the data manually, as you suggested: eset <- as(MA, 'ExpressionSet'). However, this yielded expression values from -9 to 13 and did not work:

> min(exprs(eset))
[1] -9.230704
> max(exprs(eset))
[1] 13.12851

Another question: is there a way to make arrayQualityMetrics create MA-plots and spatial plots for all arrays and not just a subset? I think that would be a nice feature, but I could not find it. For example, it would make it easier to compare MA-plots before and after normalization. As it is now, it may plot MA-plots for different arrays before and after normalization.

Best,
Daniel



On Mar 4, 2012, at 9:00 PM, Wolfgang Huber wrote:

> Dear Karen
> 
> I have just put a method into arrayQualityMetrics for 'MAList' objects.
> 
> Version 3.11.3 should come into the devel branch within 1-2 days: http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.html
> 
> I'm not doing much two-colour microarray analysis these days, so I will be interested in your experience with it, and further suggestions.
> 
> Best wishes
> 	Wolfgang
> 
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor