http://tech.groups.yahoo.com/group/microarray/ micro & macro arrays Wed, 02 Jul 2008 07:44:45 GMT jamie_zhou http://tech.groups.yahoo.com/group/microarray/message/19426 http://tech.groups.yahoo.com/group/microarray/message/19426 One-Day Intensive Microarray Data Analysis Workshop With DNA Chip Analyzer (dChip) UCLA Clinical Microarray Core is pleased to announce a one-day microarray Tue, 01 Jul 2008 08:50:27 GMT Raja M http://tech.groups.yahoo.com/group/microarray/message/19425 http://tech.groups.yahoo.com/group/microarray/message/19425 Dear Lucile,   We are using Agilent plant RNA extraction kits and it is working great for microarray applications from a wide variety of plants and Tue, 01 Jul 2008 08:49:45 GMT tanya subkhan http://tech.groups.yahoo.com/group/microarray/message/19424 http://tech.groups.yahoo.com/group/microarray/message/19424 Dear colleagues, Some time ago I have noticed a questions concerning the total number of transcripts in a single cell and transcript copies distribution within Tue, 01 Jul 2008 08:49:30 GMT Chris Seidel http://tech.groups.yahoo.com/group/microarray/message/19423 http://tech.groups.yahoo.com/group/microarray/message/19423 Hi Lucile, It would be helpful to know your protocol, so that people could comment on specific aspects. Does your protocol contain any reagents or steps for Tue, 01 Jul 2008 08:49:27 GMT Chris Seidel http://tech.groups.yahoo.com/group/microarray/message/19422 http://tech.groups.yahoo.com/group/microarray/message/19422 Hi Hussein, Poly(dA) is simply an oligonucleotide. You're best off ordering it as an oligo from a company that makes oligos. Order it on a large scale (i.e. Mon, 30 Jun 2008 07:55:12 GMT GENE-ARRAYS@... http://tech.groups.yahoo.com/group/microarray/message/19421 http://tech.groups.yahoo.com/group/microarray/message/19421 Hello all, I am trying to extract RNA from grapevine leaves. So far, RNAs are always degraded. I was wondering if anyone had any experience on this topic to Sat, 28 Jun 2008 05:08:24 GMT hussein ABDELHALEEM http://tech.groups.yahoo.com/group/microarray/message/19420 http://tech.groups.yahoo.com/group/microarray/message/19420 Hi Microarrayers I am looking for Poly(dA)-DNA (Pharmacia; Cat # 27-7988-01) or polyA (Pharmacia, cat#27-7836-01) for hybridization. I checked GE website and Thu, 26 Jun 2008 05:31:28 GMT Elliot Kleiman http://tech.groups.yahoo.com/group/microarray/message/19419 http://tech.groups.yahoo.com/group/microarray/message/19419 As long as you have at least two biological replicates the limma package will work. But you need at least two, because works by fitting a linear model to the Thu, 26 Jun 2008 05:31:24 GMT GENE-ARRAYS@... http://tech.groups.yahoo.com/group/microarray/message/19418 http://tech.groups.yahoo.com/group/microarray/message/19418 Hi Edwin, we're using BioConductor packages limma and vsn for doing what you're asking for on Agilent two-color arrays and are very happy with them. I can see Thu, 26 Jun 2008 05:31:24 GMT Kristian Almstrup http://tech.groups.yahoo.com/group/microarray/message/19417 http://tech.groups.yahoo.com/group/microarray/message/19417 Dear Edwin For the one-color agilent arrays i use the marray package. Import the gProcessedSignal as G and the gMeanSignal as R. The gProcessedSignal is Thu, 26 Jun 2008 05:31:24 GMT Willy Valdivia-Granda http://tech.groups.yahoo.com/group/microarray/message/19416 http://tech.groups.yahoo.com/group/microarray/message/19416 Hi Edwin I am not sure about a specific R package but have you tried ArrayNorm? Regards Willy Valdivia With Orion Integrated Biosciences ... Discover the Thu, 26 Jun 2008 05:31:21 GMT Dustin Potter http://tech.groups.yahoo.com/group/microarray/message/19415 http://tech.groups.yahoo.com/group/microarray/message/19415 I would recommend the limma package. The function 'read.maimages' has a setting for reading Agilent arrays. For a useful reference I would recommend the book: Thu, 26 Jun 2008 05:31:21 GMT Mayank Kumar http://tech.groups.yahoo.com/group/microarray/message/19414 http://tech.groups.yahoo.com/group/microarray/message/19414 Edwin, For one color array, It is suggested to use MAD scaling for normalization, This feature is available in LIMMA library (R package- Linear Models for Thu, 26 Jun 2008 05:31:22 GMT Gogol, Madelaine http://tech.groups.yahoo.com/group/microarray/message/19413 http://tech.groups.yahoo.com/group/microarray/message/19413 You can use the limma package. The limma user's guide is a good place to learn how to use it. Limma's not designed for one color, but you can still use it with Thu, 26 Jun 2008 05:31:21 GMT erika.melissari http://tech.groups.yahoo.com/group/microarray/message/19412 http://tech.groups.yahoo.com/group/microarray/message/19412 Hello all, I have to set an SNR (signal-to-noise ratio) filter to perform a quality control check on my microarray dual-color gene espression data. I'd like to