you get duplicate values, because there are duplicateed probe IDs on the array. Each probe set contains 16(11)-25 different values. This probes are equally distributed on the array to ascertain an equal distribution of the signal for all probe IDs. you can use the aggregate command to calculate the median (or for that point any function you would like to apply to the values.) of the different expression values Use something like that: median_rawData <- aggregate(rawData[,"columns is the data in"], list("Probe ID to merge"), FUNCTION) For the analysis of the arrays, you don't have to create a separate expressionSet object. It will be created automatically, if you normalize the data with e.g. rma or gcrma. Just follow one of the tutorials on the web or in bioconductor. They are quite easy to understand and will do everything for the beginning of the analysis. Hope this help a bit more Assa On Mon, Jan 6, 2014 at 11:57 AM, shweta bagewadi <bagewadi.shweta@gmail.com>wrote: > Hi Assa, > > here is what I want to do: > > - get the raw intensities values (as exprs object) of affybatch object > (reading from the raw data direxctly), along with the probe IDS > - get the normalized intesity values of the affybatch object > - Compare the intesities between the two generated results by looking at > the probe intensity values > > The code you sent me produced duplicate probe values, see below: > > affyIDs AFX_1_A1.CEL AFX_1_A2.CEL AFX_1_A3.CEL AFX_1_A4.CEL > 369707 1007_s_at 200 201 208 202 > 563318 1007_s_at 398 491 425 464 > 1049349 1007_s_at 427 547 528 446 > > > I already tried something simple: > > data<-ReadyAffy() > expr <- exprs(data) > eset <- new("ExpressionSet", exprs = expr, phenoData = pheno) > > Still the probe IDS are missing for the eset object. > > > Can anyone help me on how to extract raw intensity values from an affy > object. > > regards, > Shweta > ---------- Forwarded message ---------- > From: Assa Yeroslaviz <frymor@gmail.com> > Date: Mon, Jan 6, 2014 at 11:42 AM > Subject: Re: Help needed: extracting raw intensity values from Affy > To: shweta bagewadi <bagewadi.shweta@gmail.com> > > > Hi, > > here is something I did for my arrays. > It depends what kind of arrays you are using. > > Data<-ReadAffy(celfile.path="path to your arrrays" ,filenames="Name of > files" phenoData="Phenodata", verbose=TRUE) > mypm <- pm(Data) # Retrieves PM intensity values for single probes > mymm <- mm(Data) # Retrieves MM intensity values for single probes > affyIDs <- probeNames(Data) # Retrieves Affy IDs > result <- data.frame(affyIDs, mypm, mymm) # Combines the above information > in data frame > > > Hope this is helping > > cu, > Assa > > PS. > > please write to the forum (put the person than on cc), as I am sure you'll > will get help much faster. > > > > On Mon, Jan 6, 2014 at 10:35 AM, shweta bagewadi < > bagewadi.shweta@gmail.com> wrote: > >> Hi, >> >> I saw in BioC blog that u have created a thread on hopw to extract raw >> intensity values from affy object. I am also trying to do the same. >> Unfortunately, I do not see any solution in this thread. >> >> Did you find a solution for it? If yes, could you please guide me how you >> did it. >> >> Thanlks in advance. >> >> -- >> Regards, >> Shweta >> > > > > > -- > Regards, > Shweta > [[alternative HTML version deleted]]

Hi Assa, here is what I want to do: - get the raw intensities values (as exprs object) of affybatch object (reading from the raw data direxctly), along with the probe IDS - get the normalized intesity values of the affybatch object - Compare the intesities between the two generated results by looking at the probe intensity values The code you sent me produced duplicate probe values, see below: affyIDs AFX_1_A1.CEL AFX_1_A2.CEL AFX_1_A3.CEL AFX_1_A4.CEL 369707 1007_s_at 200 201 208 202 563318 1007_s_at 398 491 425 464 1049349 1007_s_at 427 547 528 446 I already tried something simple: data<-ReadyAffy() expr <- exprs(data) eset <- new("ExpressionSet", exprs = expr, phenoData = pheno) Still the probe IDS are missing for the eset object. Can anyone help me on how to extract raw intensity values from an affy object. regards, Shweta ---------- Forwarded message ---------- From: Assa Yeroslaviz <frymor@gmail.com> Date: Mon, Jan 6, 2014 at 11:42 AM Subject: Re: Help needed: extracting raw intensity values from Affy To: shweta bagewadi <bagewadi.shweta@gmail.com> Hi, here is something I did for my arrays. It depends what kind of arrays you are using. Data<-ReadAffy(celfile.path="path to your arrrays" ,filenames="Name of files" phenoData="Phenodata", verbose=TRUE) mypm <- pm(Data) # Retrieves PM intensity values for single probes mymm <- mm(Data) # Retrieves MM intensity values for single probes affyIDs <- probeNames(Data) # Retrieves Affy IDs result <- data.frame(affyIDs, mypm, mymm) # Combines the above information in data frame Hope this is helping cu, Assa PS. please write to the forum (put the person than on cc), as I am sure you'll will get help much faster. On Mon, Jan 6, 2014 at 10:35 AM, shweta bagewadi <bagewadi.shweta@gmail.com>wrote: > Hi, > > I saw in BioC blog that u have created a thread on hopw to extract raw > intensity values from affy object. I am also trying to do the same. > Unfortunately, I do not see any solution in this thread. > > Did you find a solution for it? If yes, could you please guide me how you > did it. > > Thanlks in advance. > > -- > Regards, > Shweta > -- Regards, Shweta [[alternative HTML version deleted]]

Thanks Assa. But I also found a similar function in affy which does the same. here is the code eset.no.normalization <- expresso(data, bg.correct = FALSE, bgcorrect.method = "none", bgcorrect.param = list(), normalize = FALSE, normalize.method = "constant", normalize.param = list(), pmcorrect.method = "pmonly", pmcorrect.param = list(), summary.method = "medianpolish", summary.param = list(), summary.subset = NULL, verbose = TRUE, widget = FALSE) I am still not sure if this is the right way to so it. regards, Shweta On Mon, Jan 6, 2014 at 12:21 PM, Assa Yeroslaviz <frymor@gmail.com> wrote: > you get duplicate values, because there are duplicateed probe IDs on the > array. > Each probe set contains 16(11)-25 different values. This probes are > equally distributed on the array to ascertain an equal distribution of the > signal for all probe IDs. > > you can use the aggregate command to calculate the median (or for that > point any function you would like to apply to the values.) of the different > expression values > Use something like that: > median_rawData <- aggregate(rawData[,"columns is the data in"], > list("Probe ID to merge"), FUNCTION) > > For the analysis of the arrays, you don't have to create a separate > expressionSet object. It will be created automatically, if you normalize > the data with e.g. rma or gcrma. Just follow one of the tutorials on the > web or in bioconductor. They are quite easy to understand and will do > everything for the beginning of the analysis. > > Hope this help a bit more > Assa > > > > On Mon, Jan 6, 2014 at 11:57 AM, shweta bagewadi < > bagewadi.shweta@gmail.com> wrote: > >> Hi Assa, >> >> here is what I want to do: >> >> - get the raw intensities values (as exprs object) of affybatch object >> (reading from the raw data direxctly), along with the probe IDS >> - get the normalized intesity values of the affybatch object >> - Compare the intesities between the two generated results by looking at >> the probe intensity values >> >> The code you sent me produced duplicate probe values, see below: >> >> affyIDs AFX_1_A1.CEL AFX_1_A2.CEL AFX_1_A3.CEL AFX_1_A4.CEL >> 369707 1007_s_at 200 201 208 202 >> 563318 1007_s_at 398 491 425 464 >> 1049349 1007_s_at 427 547 528 446 >> >> >> I already tried something simple: >> >> data<-ReadyAffy() >> expr <- exprs(data) >> eset <- new("ExpressionSet", exprs = expr, phenoData = pheno) >> >> Still the probe IDS are missing for the eset object. >> >> >> Can anyone help me on how to extract raw intensity values from an affy >> object. >> >> regards, >> Shweta >> ---------- Forwarded message ---------- >> From: Assa Yeroslaviz <frymor@gmail.com> >> Date: Mon, Jan 6, 2014 at 11:42 AM >> Subject: Re: Help needed: extracting raw intensity values from Affy >> To: shweta bagewadi <bagewadi.shweta@gmail.com> >> >> >> Hi, >> >> here is something I did for my arrays. >> It depends what kind of arrays you are using. >> >> Data<-ReadAffy(celfile.path="path to your arrrays" ,filenames="Name of >> files" phenoData="Phenodata", verbose=TRUE) >> mypm <- pm(Data) # Retrieves PM intensity values for single probes >> mymm <- mm(Data) # Retrieves MM intensity values for single probes >> affyIDs <- probeNames(Data) # Retrieves Affy IDs >> result <- data.frame(affyIDs, mypm, mymm) # Combines the above >> information in data frame >> >> >> Hope this is helping >> >> cu, >> Assa >> >> PS. >> >> please write to the forum (put the person than on cc), as I am sure >> you'll will get help much faster. >> >> >> >> On Mon, Jan 6, 2014 at 10:35 AM, shweta bagewadi < >> bagewadi.shweta@gmail.com> wrote: >> >>> Hi, >>> >>> I saw in BioC blog that u have created a thread on hopw to extract raw >>> intensity values from affy object. I am also trying to do the same. >>> Unfortunately, I do not see any solution in this thread. >>> >>> Did you find a solution for it? If yes, could you please guide me how >>> you did it. >>> >>> Thanlks in advance. >>> >>> -- >>> Regards, >>> Shweta >>> >> >> >> >> >> -- >> Regards, >> Shweta >> > > -- Regards, Shweta [[alternative HTML version deleted]]