Great. Thanks Jim. I will check fRMA. Shirley On Tue, Sep 25, 2012 at 11:21 AM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > Hi Shirley, > > A third option is to use fRMA, which is designed specifically for the > situation you are in right now. > > Best, > > Jim > > > > > On 9/25/2012 11:19 AM, shirley zhang wrote: >> >> Hi Jim, >> >> I kindly have a similar question: how to analyze two large affymetrix >> gene expression datasets. >> >> I have>2,000 affymetrix data in a relatively old groups. These data >> have been normalized a year ago, which took a lot of efforts >> (miss/mixed sample correction, quality check, etc.) >> >> Then recently, we got another 3000 data on the same affymetrix >> platform, but in a relatively younger group. These data have been >> normalized separately from the previous data. >> >> Now, my question is if I would like to analyze these data together >> (>5,000 samples), what are your suggestions? Two possible ways that I >> can think of are the following: >> >> 1. Re-normalize all of these 5,000 samples all together >> 2. double normalize the two datasets, for example, >> standard-transformation (z-score) or global median normalization for >> each dataset, then group them together for the down-stream statistical >> analysis. >> >> Thanks in advance for your help, >> Shirley >> >> On Tue, Sep 25, 2012 at 10:21 AM, James W. MacDonald<jmacdon at="" uw.edu=""> >> wrote: >>> >>> Hi Jun, >>> >>> On 9/25/2012 7:11 AM, Jun Han [guest] wrote: >>>> >>>> Hi, >>>> I would like to use gcrma to do a within group normalization first (30 >>>> groups in total), then input all the normalised 30 groups to do another >>>> global gcrma. >>>> Is this possible? Does the gcrma accept the inputs from the first >>>> normalisation output? >>> >>> >>> The short answer is no. When you run gcrma(), you do background >>> correction, >>> normalization, and finally summarization of the probe-level data, >>> resulting >>> in probeset-level data. In other words, you are taking the PM probes and >>> summarizing them into a single value at the probeset level (after >>> background >>> correcting and normalizing). >>> >>> Since gcrma() expects you to be inputting an AffyBatch containing PM and >>> MM >>> probe data, it fails when you input an ExpressionSet containing >>> summarized >>> probeset level data. >>> >>> I assume you are trying to combine two groups that you think should not >>> be >>> normalized and summarized together. This leads to two questions - first, >>> why >>> don't you think these data can be combined prior to the gcrma() step, and >>> second, if the answer to the first question is because of a batch effect, >>> have you looked at e.g., sva or comBat? >>> >>> Best, >>> >>> Jim >>> >>> >>>> Many thanks. >>>> Jun >>>> >>>> -- output of sessionInfo(): >>>> >>>>> gcrma12<-gcrma(gcrma1,gcrma2) >>>> >>>> Error in function (classes, fdef, mtable) : >>>> unable to find an inherited method for function "indexProbes", for >>>> signature "ExpressionSet", "character" >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at 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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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 > -- Xiaoling (Shirley) Zhang M.D., Ph.D. Boston University, Boston, MA Tel: (857) 233-9862 Email: zhangxl at bu.edu