[BioC] NOISeq-real input parameters

papori [guest] guest at bioconductor.org
Mon Mar 19 10:38:00 CET 2012

Hi all, 
i am using NOISeq with biological replicates.(i saw the Warning: NOISeq for biological replicates has not been tested yet. In case you use it, we will be very grateful to receive any feedback from you! , so, it will be a feedback in the end..)

I have 2 conditions with 3 replicates for each.
I normalized my data by using "tmm".
i execute NOISeq as:
myresults <- noiseq(mytmmdata_a,mytmmdata_na,repl = "bio" , k=0.5 , norm="tmm" , long=1000, q=0.8, nss=0)

My question is on the "q" parameter.
Usually significant is when p.v = 0.05.
What "q" value equal for that?
What is the "q" test? how calculate?


 -- output of sessionInfo(): 

R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C                 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_2.4.3  limma_3.10.3

loaded via a namespace (and not attached):
 [1] annotate_1.32.2       AnnotationDbi_1.16.19 Biobase_2.14.0        DBI_0.2-5             DESeq_1.6.1          
 [6] genefilter_1.36.0     geneplotter_1.32.1    grid_2.14.0           IRanges_1.12.6        RColorBrewer_1.0-5   
[11] RSQLite_0.11.1        splines_2.14.0        survival_2.36-12      tools_2.14.0          xtable_1.7-0 

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