Johanne [[alternative HTML version deleted]]

Hi, I would like to flag bad spots, but I'm not sure what's the criteria for 'BAD'. Please give me some advice Thanks a lots zhao

Hello, In our Lab we are starting to run microarray analysis by using the mArray package. We followed the 'Biologists guide to using Bioconductor' published Nov 2002 by C. Bye: http://www.people.fas.harvard.edu/~grosu/downloads/bioconductor_manual .pdf Following the instructions we modified the gal file introducing a column "controls" to specify the blanks and N/A spots. To vizualize these controls in MA plots we try this R code (as indicated in the guide): blanks<-maText(subset=maControls(christian.raw[,1]) == "EMPTY") , labels="o", col="purple") maPlot(christian.raw[,1], text.func = blanks) We tried to exchange "EMPTY" by any control specified and even tried "Control" In any case this resulted in a "syntax error" We crosschecked whether these controls are accesible with the following code: maImage(christian.raw[,1], x="maControls) There we get a warning message and no plot. Here is an extract of our modified gal file. To our knowledge this should be ok. Block Row Column ID Name Controls 4 21 5 H200021155 Homo sapiens cDNA FLJ30327 fis OK 4 21 7 H200021179 Homo sapiens cDNA FLJ32985 fi OK 4 21 8 H200021185 Homo sapiens cDNA FLJ30893 fis OK 4 21 9 n/a n/a NA 4 21 16 n/a n/a NA 4 22 3 Blank Blank EMPTY 4 22 5 Blank Blank EMPTY Does anybody know how to handle this operation (visualization of control spots specified in the gal file) or if we made some other mistake? Thanks (in advance) for help, Christian Riedel Ph.D. student

Hi, Need your help in the following: I am interedted in the software package - affy (developmental). I have downloaded also. I Requrest you that how to run the package. There is no set up/exe file. I shall be very much grateful if you could kindly help in instructing me that how to use this software package. Thanks & Regards Muthu, S _________________________________________________________________ Garfield on your mobile. Download now. http://server1.msn.co.in/sp03/gprs/ How cool can life get?