Question: How to print out normalized Cy5 and Cy3 signals
0
7.5 years ago by
JiangMei10
JiangMei10 wrote:
Hi All. Sorry to bother you. I used limma package to normalize my two-color microarray data. I want to export the normalized Cy5 and Cy3 signals. Does anyone know how to do that? Thanks very much in advance. Best, Mei [[alternative HTML version deleted]]
microarray limma • 450 views
modified 7.5 years ago by Belinda Phipson130 • written 7.5 years ago by JiangMei10
Answer: How to print out normalized Cy5 and Cy3 signals
0
7.5 years ago by
Belinda Phipson130 wrote:
Hi Mei Check the names of your data object: > names(data) to figure out where the normalized data is and then use the > write.csv(data$...,file="norm.csv") which can write matrices or data frames to a file which can be opened in excel. Cheers, Belinda -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of JiangMei Sent: Saturday, 16 June 2012 5:05 AM To: bioconductor at r-project.org Subject: [BioC] How to print out normalized Cy5 and Cy3 signals Hi All. Sorry to bother you. I used limma package to normalize my two-color microarray data. I want to export the normalized Cy5 and Cy3 signals. Does anyone know how to do that? Thanks very much in advance. Best, Mei [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}} ADD COMMENTlink written 7.5 years ago by Belinda Phipson130 Hi, I think one additional step before doing what Belinda suggested is to run RG.MA() because after normalization in limma you get MAlist and Cy5 and Cy3 signals are not in MAlist. You need to convert it back to RGlist. Kind regards, Yong On Mon, Jun 18, 2012 at 2:54 AM, Belinda Phipson <phipson at="" wehi.edu.au=""> wrote: > Hi Mei > > Check the names of your data object: >> names(data) > to figure out where the normalized data is and then use the >> write.csv(data$...,file="norm.csv") > which can write matrices or data frames to a file which can be opened in > excel. > > Cheers, > Belinda > > -----Original Message----- > From: bioconductor-bounces at r-project.org > [mailto:bioconductor-bounces at r-project.org] On Behalf Of JiangMei > Sent: Saturday, 16 June 2012 5:05 AM > To: bioconductor at r-project.org > Subject: [BioC] How to print out normalized Cy5 and Cy3 signals > > > Hi All. Sorry to bother you. > > I used limma package to normalize my two-color microarray data. I want to > export the normalized Cy5 and Cy3 signals. Does anyone know how to do that? > Thanks very much in advance. > > > Best, Mei > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 > > > ______________________________________________________________________ > The information in this email is confidential and intend...{{dropped:4}} > > _______________________________________________ > 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