Question: Replicates array
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gravatar for Paola Sgado'
15.5 years ago by
Paola Sgado'20
Paola Sgado'20 wrote:
Hi I just started to work with oligonucleotide microarray and I would like to have suggestions on the methods I should use to analyse the data. I have three duplicates done in two different places, so they look very different in terms of background and signal intensities. Since I'm not going to have more duplicates I would like to get the most information possible from these, even if I do know that it is not the perfect experimental design! My question is, if the chips are very different, should I normalize them separately (for example make to groups)? Does it make sense to compare them between two gruops if they are normalised separately? Should I just compare the differentially expressed genes lists coming from the two different group of duplicates?? Thank you for your help!! Paola
microarray • 519 views
ADD COMMENTlink modified 15.5 years ago by mai98ftu@studserv.uni-leipzig.de140 • written 15.5 years ago by Paola Sgado'20
Answer: Replicates array
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gravatar for mai98ftu@studserv.uni-leipzig.de
15.5 years ago by
Hi Paola, For preprocessing I would suggest to use RMA (i.e. RMA background correction + quantile normalization + medianpolish) or VSN + medianpolish. I would normalize all 6 arrys together. I don't think it's a good idea to normalize the two groups separately. > Should I just compare the differentially expressed genes lists coming > from the two different group of duplicates?? I don't understand. Wouldn't it be just one list? Johannes Quoting Paola Sgado' <sgadop@yahoo.it>: > Hi > I just started to work with oligonucleotide microarray and I would like > > to have suggestions on the methods I should use to analyse the data. > > I have three duplicates done in two different places, so they look very > > different in terms of background and signal intensities. Since I'm not > going to have more duplicates I would like to get the most information > possible from these, even if I do know that it is not the perfect > experimental design! > > My question is, if the chips are very different, should I normalize > them separately (for example make to groups)? Does it make sense to > compare them between two gruops if they are normalised separately? > Should I just compare the differentially expressed genes lists coming > from the two different group of duplicates?? > > Thank you for your help!! > Paola > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 15.5 years ago by mai98ftu@studserv.uni-leipzig.de140
Hi, I didn't explain the things properly, sorry! What I have is three different treatments, each one with its own control. Of these 6 chips I have three duplicates done in two different places. At the end what I compare is treated vs untreated, so I can have list of differentially expressed genes without considering the replicates. My question is: Do I need to process (rma) all the chips together to be able to compare the replicates? Does it change the list of differentially expressed genes if I do separate rma for the different replicates? Thanks again for your help Paola
ADD REPLYlink written 15.5 years ago by Paola Sgado'20
Hi All, Is there any way to combine two or more marrayRaw class objects? For example, if I use read.GenePix to read in two different cDNA datasets into two different marrayRaw objects, and later on I want to combine both together into one single object. Any advice? Thank you Tzu Paola Sgado' wrote: > Hi, > I didn't explain the things properly, sorry! > > What I have is three different treatments, each one with its own > control. Of these 6 chips I have three duplicates done in two > different places. At the end what I compare is treated vs untreated, > so I can have list of differentially expressed genes without > considering the replicates. My question is: Do I need to process (rma) > all the chips together to be able to compare the replicates? Does it > change the list of differentially expressed genes if I do separate rma > for the different replicates? > > Thanks again for your help > Paola > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- Tzu L. Phang, Ph.D. 303-315-1583 http://compbio.uchsc.edu/Hunter_lab/Phang
ADD REPLYlink written 15.5 years ago by Tzulip Phang40
Hi Tzulip, Are they from the same print-run? If yes, you can try the function cbind after installing the developmental version of marrayClasses. Cheers Jean On Wed, 10 Mar 2004, Tzulip Phang wrote: > Hi All, > > Is there any way to combine two or more marrayRaw class objects? For > example, if I use read.GenePix to read in two different cDNA datasets > into two different marrayRaw objects, and later on I want to combine > both together into one single object. > > Any advice? > > Thank you > > Tzu > > Paola Sgado' wrote: > > > Hi, > > I didn't explain the things properly, sorry! > > > > What I have is three different treatments, each one with its own > > control. Of these 6 chips I have three duplicates done in two > > different places. At the end what I compare is treated vs untreated, > > so I can have list of differentially expressed genes without > > considering the replicates. My question is: Do I need to process (rma) > > all the chips together to be able to compare the replicates? Does it > > change the list of differentially expressed genes if I do separate rma > > for the different replicates? > > > > Thanks again for your help > > Paola > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > -- > Tzu L. Phang, Ph.D. > 303-315-1583 > http://compbio.uchsc.edu/Hunter_lab/Phang > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD REPLYlink written 15.5 years ago by Jean Yee Hwa Yang920
Hi Jean, Actually I have found the solution throught the searchable mail-list where someone placed the source code for cbindmarrayRaw which will do the job. Thank you Tzu Jean Yee Hwa Yang wrote: >Hi Tzulip, > >Are they from the same print-run? If yes, you can try the function cbind >after installing the developmental version of marrayClasses. > >Cheers > >Jean > >On Wed, 10 Mar 2004, Tzulip Phang wrote: > > > >>Hi All, >> >>Is there any way to combine two or more marrayRaw class objects? For >>example, if I use read.GenePix to read in two different cDNA datasets >>into two different marrayRaw objects, and later on I want to combine >>both together into one single object. >> >>Any advice? >> >>Thank you >> >>Tzu >> >>Paola Sgado' wrote: >> >> >> >>>Hi, >>>I didn't explain the things properly, sorry! >>> >>>What I have is three different treatments, each one with its own >>>control. Of these 6 chips I have three duplicates done in two >>>different places. At the end what I compare is treated vs untreated, >>>so I can have list of differentially expressed genes without >>>considering the replicates. My question is: Do I need to process (rma) >>>all the chips together to be able to compare the replicates? Does it >>>change the list of differentially expressed genes if I do separate rma >>>for the different replicates? >>> >>>Thanks again for your help >>>Paola >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor@stat.math.ethz.ch >>>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >>> >>> >>> >>-- >>Tzu L. Phang, Ph.D. >>303-315-1583 >>http://compbio.uchsc.edu/Hunter_lab/Phang >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >> >> > > > > -- Tzu L. Phang, Ph.D. 303-315-1583 http://compbio.uchsc.edu/Hunter_lab/Phang [[alternative HTML version deleted]]
ADD REPLYlink written 15.5 years ago by Tzulip Phang40
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