Hi Jim,  Many thanks for your quick and very comprehensive response. 
>From your comments, I have one more question related:
(1) I understand your comments about the intron control transcripts, but I do not fully understand the rescue transcript category that I have also obtained in my topTable transcripts.   
No need to send the function, but thanks in any case for offering.
Regards,
Maria
> Date: Fri, 29 Nov 2013 09:04:20 -0500
> From: jmacdon@uw.edu
> To: guest@bioconductor.org
> CC: bioconductor@r-project.org; mmaqueda@live.com
> Subject: Re: [BioC] Analysis of Affymetrix Human Gene 2.0 ST arrays
> 
> Hi Maria,
> 
> 
> On 11/29/2013 6:18 AM, María Maqueda [guest] wrote:
> > Dear all,
> >    
> >   I am analyzing a set of Affymetrix Human Gene 2.0 ST arrays, this is my first time working with this type of arrays so I have a few general questions. I would very much appreciate any advice you could give.
> >
> > (1) I have obtained different lists of differentially expressed genes (using eBayes() from limma). In those lists, some control transcripts are popping up (i.e normgene -> intron category among other categories). I was not expecting this type of transcripts at this point. In theory after normalization, no control transcripts should appear, am I right? Have you experienced this?
> > I have read that one possibility is to use getMainProbes before topTable selection but I wonder if there could be something wrong from the beginning with my normalization process (I have used rma() â€“ transcript level - from oligo). What is your opinion?
> 
> I don't think it has anything to do with the normalization. Instead, I 
> think it is a combination of poorly designed probes and highly expressed 
> genes for which there are sufficient unprocessed mRNA transcripts that 
> still have their introns intact (remember that the processing of samples 
> stops all enzymatic activity very quickly as a first step, so any mRNA 
> that is in the process of being transcribed, or is just finishing 
> transcription will likely still have introns).
> 
> >
> > (2) This type of arrays also includes lincRNA transcripts and I am interested in considering them for my analysis. The thing is that I am using hugene20sttranscriptcluster.db for annotation and these lincRNA are not included. Would this library be able to handle them?
> 
> Hypothetically yes, as of now not really. It doesn't seem like that many 
> have been annotated with Entrez Gene IDs, and until that happens they 
> won't appear in the annotation packages. And even for those that do have 
> Entrez Gene IDs, the information stops there - you go to NCBI and it 
> just says that the lincRNA is supposed to exist, but nothing else.
> 
> >
> > (3) I tried to make my own annotation package thru makeDBPackage based on .csv annotation file from Affy but I got an errorâ€¦:  Error in `[.data.frame`(csvFile, , GenBank IDName) : undefined columns selected
> > I have already read in this mailing list that makeDBPackage may expect a HGU133plus2 annotation â€œstyleâ€. Would the library annotationForge be able to handle this?
> 
> AnnotationForge cannot handle the csv files for these arrays directly, 
> as they are completely different from the old style 3'-biased arrays 
> like the hgu133plus2 that you mention. I have a function I can give you 
> to make the input file for the annotation package, but I don't think it 
> is worth it because it would be the function that I already used to make 
> the annotation package you can get from BioC. So you could go through 
> all the effort to make something you can already get.
> 
> But if you want it, I will send it to you.
> 
> Best,
> 
> Jim
> 
> 
> >
> >
> > Many thanks in advance for any help!
> >
> >
> > MarÃ­a Maqueda
> >
> > Biomedical Engineering Research Centre (CREB)
> > Universitat PolitÃ¨cnica de Catalunya (UPC)
> >
> >   -- output of sessionInfo():
> >
> >> sessionInfo()
> > R version 3.0.1 (2013-05-16)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> >
> > locale:
> > [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
> > [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
> > [5] LC_TIME=Spanish_Spain.1252
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> >   [1] human.db0_2.9.0                       AnnotationForge_1.2.2
> >   [3] hugene20sttranscriptcluster.db_2.12.1 org.Hs.eg.db_2.9.0
> >   [5] AnnotationDbi_1.22.6                  BiocInstaller_1.12.0
> >   [7] limma_3.16.8                          pd.hugene.2.0.st_3.8.0
> >   [9] oligo_1.24.2                          Biobase_2.20.1
> > [11] oligoClasses_1.22.0                   BiocGenerics_0.6.0
> > [13] RSQLite_0.11.4                        DBI_0.2-7
> >
> > loaded via a namespace (and not attached):
> >   [1] affxparser_1.32.3     affyio_1.28.0         annotate_1.38.0
> >   [4] Biostrings_2.28.0     bit_1.1-10            codetools_0.2-8
> >   [7] ff_2.2-12             foreach_1.4.1         genefilter_1.42.0
> > [10] GenomicRanges_1.12.5  IRanges_1.18.4        iterators_1.0.6
> > [13] preprocessCore_1.22.0 splines_3.0.1         stats4_3.0.1
> > [16] survival_2.37-4       tools_3.0.1           XML_3.98-1.1
> > [19] xtable_1.7-1          zlibbioc_1.6.0
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 
 		 	   		  
	[[alternative HTML version deleted]]

