Hello, I have 2 one color Beadarray(HumanRef8 v3) and i'm intrested in comparing diffirentially expressed genes at bead level. Raw file is a 4 column text file Code Grn GrnX GrnY 10008 750 1376.448 8700.565 10008 682 1781.302 12418.69 10008 510 1555.273 6437.563 10008 714 910.3025 1081.659 There's also an annotation file (bgx) I would like to generate a table sample 1 sample 2 bead 1 bead 2 . bead m1 bead 1 bead 2 . bead m2 probeid 1 probeid 2 . probeid n any one had the chance to do this before or have an idea on how to do it ? Thanks in advance. Regards, Ramzi [[alternative HTML version deleted]]

Hi Ramzi, The beadarray package is designed to handle Illumina array data at the bead-level. Most of its functionality is directed at performing preprocessing and QA at the bead-level, before the data is summarized by probe type. These summarized values can then be passed to packages such a limma for differential expression analysis. I hope that's of some help, Mike Smith Ramzi TEMANNI wrote: > Hello, > I have 2 one color Beadarray(HumanRef8 v3) and i'm intrested in comparing > diffirentially expressed genes at bead level. > Raw file is a 4 column text file > Code Grn GrnX GrnY 10008 750 1376.448 8700.565 10008 682 1781.302 > 12418.69 10008 510 1555.273 6437.563 10008 714 910.3025 1081.659 There's > also an annotation file (bgx) > I would like to generate a table > sample 1 sample 2 bead 1 bead 2 ?. bead m1 bead 1 bead 2 ?. bead > m2 probeid 1 probeid 2 ?. > probeid > n > > any one had the chance to do this before or have an idea on how to do it ? > > Thanks in advance. > Regards, > Ramzi > > [[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