Replicates array

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Paola Sgado' ▴ 20

@paola-sgado-664

Last seen 10.2 years ago

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 Microarray • 1.4k views

ADD COMMENT • link updated 20.7 years ago by mai98ftu@studserv.uni-leipzig.de ▴ 140 • written 20.7 years ago by Paola Sgado' ▴ 20

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mai98ftu@studserv.uni-leipzig.de ▴ 140

@mai98ftustudservuni-leipzigde-338

Last seen 10.2 years ago

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 COMMENT • link 20.7 years ago mai98ftu@studserv.uni-leipzig.de ▴ 140

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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 REPLY • link 20.7 years ago Paola Sgado' ▴ 20

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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 REPLY • link 20.7 years ago Tzulip Phang ▴ 40

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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 REPLY • link 20.7 years ago Jean Yee Hwa Yang ▴ 920

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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 REPLY • link 20.7 years ago Tzulip Phang ▴ 40

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