Question: Import files from Applied Biosystems 7900HT?
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gravatar for Brian Diggs
8.9 years ago by
Brian Diggs30
Brian Diggs30 wrote:
Though I have used R for a few years, I am starting a project where this is my first real use of Bioconductor and I am having a problem reading expression data from files. The files are created by an Applied Biosystems 7900HT machine. I found the ABarray package, but that only claims to work with AB1700 data. On a lark, I tried to use it for my data, but got an error Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 2 did not have 3 elements which seems consistent with a file not being in the right format. Can anyone tell me if there exists a package that can read this data into an ExpressionSet? Or has anyone even used Bioconductor with data from this, and, if so, what needs to be done to import the data? -- Brian Diggs Senior Research Associate, Department of Surgery, Oregon Health & Science University
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ADD COMMENTlink modified 8.9 years ago by Heidi Dvinge2.0k • written 8.9 years ago by Brian Diggs30
Answer: Import files from Applied Biosystems 7900HT?
0
gravatar for Heidi Dvinge
8.9 years ago by
Heidi Dvinge2.0k
Heidi Dvinge2.0k wrote:
Hello Brian, wait, is your data from a microarray or a qPCR plate? I think the 7900HT machine is what Applied Biosystems use with the TaqMan Low Density Cards. If so, you can use the package HTqPCR for reading in an processing the data. The basic data structure there is a qPCRSet object, which is similar to ExpressionSet, only designed for qPCR data. If my memory is failing my regarding the 7900HT and you actually have microarray data, then you should be able to read them into R using e.g. the package limma. HTH \Heidi > > > > Though I have used R for a few years, I am starting a project where this > is my first real use of Bioconductor and I am having a problem reading > expression data from files. The files are created by an Applied > Biosystems 7900HT machine. I found the ABarray package, but that only > claims to work with AB1700 data. On a lark, I tried to use it for my > data, but got an error > > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, > na.strings, : > line 2 did not have 3 elements > > which seems consistent with a file not being in the right format. Can > anyone tell me if there exists a package that can read this data into an > ExpressionSet? Or has anyone even used Bioconductor with data from > this, and, if so, what needs to be done to import the data? > > -- > Brian Diggs > Senior Research Associate, Department of Surgery, Oregon Health & > Science University > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 8.9 years ago by Heidi Dvinge2.0k
On Apr 21, 2010, at 2:54 PM, Heidi Dvinge wrote: > Hello Brian, > > wait, is your data from a microarray or a qPCR plate? I think the > 7900HT > machine is what Applied Biosystems use with the TaqMan Low Density > Cards. > If so, you can use the package HTqPCR for reading in an processing the > data. The basic data structure there is a qPCRSet object, which is > similar > to ExpressionSet, only designed for qPCR data. > > If my memory is failing my regarding the 7900HT and you actually have > microarray data, then you should be able to read them into R using > e.g. > the package limma. Greetings Having just gone through a similar process, I found it depends a lot on how the data were processed by the SDS software if you have 7900HT data. Do you have the original *.sds files, or *.sdm or some other format? I read the original *.sds files into the RQ manager software, set the window to be 'Plate Centric' and then I could export 'Results' and the files had the format expected by HTqPCR. These were not the settings I got when I first started the software and it took some trial and error to figure it out. Cheers Mike > > HTH > \Heidi >> >> >> >> Though I have used R for a few years, I am starting a project where >> this >> is my first real use of Bioconductor and I am having a problem >> reading >> expression data from files. The files are created by an Applied >> Biosystems 7900HT machine. I found the ABarray package, but that >> only >> claims to work with AB1700 data. On a lark, I tried to use it for my >> data, but got an error >> >> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >> na.strings, : >> line 2 did not have 3 elements >> >> which seems consistent with a file not being in the right format. >> Can >> anyone tell me if there exists a package that can read this data >> into an >> ExpressionSet? Or has anyone even used Bioconductor with data from >> this, and, if so, what needs to be done to import the data? >> >> -- >> Brian Diggs >> Senior Research Associate, Department of Surgery, Oregon Health & >> Science University >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806
ADD REPLYlink written 8.9 years ago by Michael Muratet420
On 4/21/2010 2:38 PM, Michael Muratet wrote: > > On Apr 21, 2010, at 2:54 PM, Heidi Dvinge wrote: > >> Hello Brian, >> >> wait, is your data from a microarray or a qPCR plate? I think the 7900HT >> machine is what Applied Biosystems use with the TaqMan Low Density Cards. >> If so, you can use the package HTqPCR for reading in an processing the >> data. The basic data structure there is a qPCRSet object, which is >> similar >> to ExpressionSet, only designed for qPCR data. >> >> If my memory is failing my regarding the 7900HT and you actually have >> microarray data, then you should be able to read them into R using e.g. >> the package limma. > > Greetings > > Having just gone through a similar process, I found it depends a lot on > how the data were processed by the SDS software if you have 7900HT data. > Do you have the original *.sds files, or *.sdm or some other format? I > read the original *.sds files into the RQ manager software, set the > window to be 'Plate Centric' and then I could export 'Results' and the > files had the format expected by HTqPCR. These were not the settings I > got when I first started the software and it took some trial and error > to figure it out. > > Cheers > > Mike Thank you for the information, Heidi and Mike, especially given how vague I was. The data is from Taqman Low Density Arrays and is qPCR data. I am not doing the runs myself, though I have access to the person who is. We are still working out details in workflow. The files I have been getting thus far are, I think, SDS files. They have a .txt extension, but the first few lines are: SDS 2.3 AQ Results 1.0 Filename TLDA-M10-21T_ALL cDNA042110 PlateID Assay Type Absolute Quantification Run DateTime 4/21/10 1:28:40 PM I don't have a copy of the RQ manager software myself, but I know it is on the computer running the machine. I'll see about getting a copy of it for myself or getting some time to do the conversion on the original computer and see about importing the data using HTqPCR::readCtData then. >> >> HTH >> \Heidi >>> >>> >>> >>> Though I have used R for a few years, I am starting a project where this >>> is my first real use of Bioconductor and I am having a problem reading >>> expression data from files. The files are created by an Applied >>> Biosystems 7900HT machine. I found the ABarray package, but that only >>> claims to work with AB1700 data. On a lark, I tried to use it for my >>> data, but got an error >>> >>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>> na.strings, : >>> line 2 did not have 3 elements >>> >>> which seems consistent with a file not being in the right format. Can >>> anyone tell me if there exists a package that can read this data into an >>> ExpressionSet? Or has anyone even used Bioconductor with data from >>> this, and, if so, what needs to be done to import the data? >>> >>> -- >>> Brian Diggs >>> Senior Research Associate, Department of Surgery, Oregon Health & >>> Science University >>> > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > mmuratet-Sy0TgEBENMiWTJ9x5QRIJA at public.gmane.org > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > -- Brian Diggs Senior Research Associate, Department of Surgery, Oregon Health & Science University
ADD REPLYlink written 8.9 years ago by Brian Diggs30
> On 4/21/2010 2:38 PM, Michael Muratet wrote: >> >> On Apr 21, 2010, at 2:54 PM, Heidi Dvinge wrote: >> >>> Hello Brian, >>> >>> wait, is your data from a microarray or a qPCR plate? I think the >>> 7900HT >>> machine is what Applied Biosystems use with the TaqMan Low Density >>> Cards. >>> If so, you can use the package HTqPCR for reading in an processing the >>> data. The basic data structure there is a qPCRSet object, which is >>> similar >>> to ExpressionSet, only designed for qPCR data. >>> >>> If my memory is failing my regarding the 7900HT and you actually have >>> microarray data, then you should be able to read them into R using e.g. >>> the package limma. >> >> Greetings >> >> Having just gone through a similar process, I found it depends a lot on >> how the data were processed by the SDS software if you have 7900HT data. >> Do you have the original *.sds files, or *.sdm or some other format? I >> read the original *.sds files into the RQ manager software, set the >> window to be 'Plate Centric' and then I could export 'Results' and the >> files had the format expected by HTqPCR. These were not the settings I >> got when I first started the software and it took some trial and error >> to figure it out. >> >> Cheers >> >> Mike > > Thank you for the information, Heidi and Mike, especially given how > vague I was. The data is from Taqman Low Density Arrays and is qPCR data. > > I am not doing the runs myself, though I have access to the person who > is. We are still working out details in workflow. The files I have > been getting thus far are, I think, SDS files. They have a .txt > extension, but the first few lines are: > > SDS 2.3 AQ Results 1.0 > Filename TLDA-M10-21T_ALL cDNA042110 > PlateID > Assay Type Absolute Quantification > Run DateTime 4/21/10 1:28:40 PM > > I don't have a copy of the RQ manager software myself, but I know it is > on the computer running the machine. I'll see about getting a copy of > it for myself or getting some time to do the conversion on the original > computer and see about importing the data using HTqPCR::readCtData then. > Hello Brian, ExpressionSet objects (and the packages that use them) are specifically designed for microarray data. So if you have qPCR data you're better of using HTqPCR or some other package designed for qPCR. It looks like you have standard SDS format. In that case you don't need to do any conversions to read the data into HTqPCR. If you have the latest version, 1.1.4, there's a parameter called "SDS" in readCtData. If you set that to TRUE it should work. HTH \Heidi >>> >>> HTH >>> \Heidi >>>> >>>> >>>> >>>> Though I have used R for a few years, I am starting a project where >>>> this >>>> is my first real use of Bioconductor and I am having a problem reading >>>> expression data from files. The files are created by an Applied >>>> Biosystems 7900HT machine. I found the ABarray package, but that only >>>> claims to work with AB1700 data. On a lark, I tried to use it for my >>>> data, but got an error >>>> >>>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>>> na.strings, : >>>> line 2 did not have 3 elements >>>> >>>> which seems consistent with a file not being in the right format. Can >>>> anyone tell me if there exists a package that can read this data into >>>> an >>>> ExpressionSet? Or has anyone even used Bioconductor with data from >>>> this, and, if so, what needs to be done to import the data? >>>> >>>> -- >>>> Brian Diggs >>>> Senior Research Associate, Department of Surgery, Oregon Health & >>>> Science University >>>> >> >> Michael Muratet, Ph.D. >> Senior Scientist >> HudsonAlpha Institute for Biotechnology >> mmuratet-Sy0TgEBENMiWTJ9x5QRIJA at public.gmane.org >> (256) 327-0473 (p) >> (256) 327-0966 (f) >> >> Room 4005 >> 601 Genome Way >> Huntsville, Alabama 35806 >> > > -- > Brian Diggs > Senior Research Associate, Department of Surgery, Oregon Health & > Science University > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 8.9 years ago by Heidi Dvinge2.0k
On Apr 22, 2010, at 3:50 PM, Heidi Dvinge wrote: >> On 4/21/2010 2:38 PM, Michael Muratet wrote: >>> >>> On Apr 21, 2010, at 2:54 PM, Heidi Dvinge wrote: >>> >>>> Hello Brian, >>>> >>>> wait, is your data from a microarray or a qPCR plate? I think the >>>> 7900HT >>>> machine is what Applied Biosystems use with the TaqMan Low Density >>>> Cards. >>>> If so, you can use the package HTqPCR for reading in an >>>> processing the >>>> data. The basic data structure there is a qPCRSet object, which is >>>> similar >>>> to ExpressionSet, only designed for qPCR data. >>>> >>>> If my memory is failing my regarding the 7900HT and you actually >>>> have >>>> microarray data, then you should be able to read them into R >>>> using e.g. >>>> the package limma. >>> >>> Greetings >>> >>> Having just gone through a similar process, I found it depends a >>> lot on >>> how the data were processed by the SDS software if you have 7900HT >>> data. >>> Do you have the original *.sds files, or *.sdm or some other >>> format? I >>> read the original *.sds files into the RQ manager software, set the >>> window to be 'Plate Centric' and then I could export 'Results' and >>> the >>> files had the format expected by HTqPCR. These were not the >>> settings I >>> got when I first started the software and it took some trial and >>> error >>> to figure it out. >>> >>> Cheers >>> >>> Mike >> >> Thank you for the information, Heidi and Mike, especially given how >> vague I was. The data is from Taqman Low Density Arrays and is >> qPCR data. >> >> I am not doing the runs myself, though I have access to the person >> who >> is. We are still working out details in workflow. The files I have >> been getting thus far are, I think, SDS files. They have a .txt >> extension, but the first few lines are: >> >> SDS 2.3 AQ Results 1.0 >> Filename TLDA-M10-21T_ALL cDNA042110 >> PlateID >> Assay Type Absolute Quantification >> Run DateTime 4/21/10 1:28:40 PM >> >> I don't have a copy of the RQ manager software myself, but I know >> it is >> on the computer running the machine. I'll see about getting a copy >> of >> it for myself or getting some time to do the conversion on the >> original >> computer and see about importing the data using HTqPCR::readCtData >> then. >> > Hello Brian, > > ExpressionSet objects (and the packages that use them) are > specifically > designed for microarray data. So if you have qPCR data you're better > of > using HTqPCR or some other package designed for qPCR. > > It looks like you have standard SDS format. In that case you don't > need to > do any conversions to read the data into HTqPCR. If you have the > latest > version, 1.1.4, there's a parameter called "SDS" in readCtData. If > you set > that to TRUE it should work. Hi guys I would check and make sure you have a Ct column in the data. Some SDS export settings will produce it (i.e., the plate-centric view) and some won't in favor of ddCt and RQ. The header data shows up in them all. Mike > > HTH > \Heidi > >>>> >>>> HTH >>>> \Heidi >>>>> >>>>> >>>>> >>>>> Though I have used R for a few years, I am starting a project >>>>> where >>>>> this >>>>> is my first real use of Bioconductor and I am having a problem >>>>> reading >>>>> expression data from files. The files are created by an Applied >>>>> Biosystems 7900HT machine. I found the ABarray package, but that >>>>> only >>>>> claims to work with AB1700 data. On a lark, I tried to use it >>>>> for my >>>>> data, but got an error >>>>> >>>>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>>>> na.strings, : >>>>> line 2 did not have 3 elements >>>>> >>>>> which seems consistent with a file not being in the right >>>>> format. Can >>>>> anyone tell me if there exists a package that can read this data >>>>> into >>>>> an >>>>> ExpressionSet? Or has anyone even used Bioconductor with data from >>>>> this, and, if so, what needs to be done to import the data? >>>>> >>>>> -- >>>>> Brian Diggs >>>>> Senior Research Associate, Department of Surgery, Oregon Health & >>>>> Science University >>>>> >>> >>> Michael Muratet, Ph.D. >>> Senior Scientist >>> HudsonAlpha Institute for Biotechnology >>> mmuratet-Sy0TgEBENMiWTJ9x5QRIJA at public.gmane.org >>> (256) 327-0473 (p) >>> (256) 327-0966 (f) >>> >>> Room 4005 >>> 601 Genome Way >>> Huntsville, Alabama 35806 >>> >> >> -- >> Brian Diggs >> Senior Research Associate, Department of Surgery, Oregon Health & >> Science University >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806
ADD REPLYlink written 8.9 years ago by Michael Muratet420
On 4/22/2010 2:08 PM, Michael Muratet wrote: > > On Apr 22, 2010, at 3:50 PM, Heidi Dvinge wrote: > >>> On 4/21/2010 2:38 PM, Michael Muratet wrote: >>>> >>>> On Apr 21, 2010, at 2:54 PM, Heidi Dvinge wrote: >>>> >>>>> Hello Brian, >>>>> >>>>> wait, is your data from a microarray or a qPCR plate? I think the >>>>> 7900HT >>>>> machine is what Applied Biosystems use with the TaqMan Low Density >>>>> Cards. >>>>> If so, you can use the package HTqPCR for reading in an processing the >>>>> data. The basic data structure there is a qPCRSet object, which is >>>>> similar >>>>> to ExpressionSet, only designed for qPCR data. >>>>> >>>>> If my memory is failing my regarding the 7900HT and you actually have >>>>> microarray data, then you should be able to read them into R using >>>>> e.g. >>>>> the package limma. >>>> >>>> Greetings >>>> >>>> Having just gone through a similar process, I found it depends a lot on >>>> how the data were processed by the SDS software if you have 7900HT >>>> data. >>>> Do you have the original *.sds files, or *.sdm or some other format? I >>>> read the original *.sds files into the RQ manager software, set the >>>> window to be 'Plate Centric' and then I could export 'Results' and the >>>> files had the format expected by HTqPCR. These were not the settings I >>>> got when I first started the software and it took some trial and error >>>> to figure it out. >>>> >>>> Cheers >>>> >>>> Mike >>> >>> Thank you for the information, Heidi and Mike, especially given how >>> vague I was. The data is from Taqman Low Density Arrays and is qPCR >>> data. >>> >>> I am not doing the runs myself, though I have access to the person who >>> is. We are still working out details in workflow. The files I have >>> been getting thus far are, I think, SDS files. They have a .txt >>> extension, but the first few lines are: >>> >>> SDS 2.3 AQ Results 1.0 >>> Filename TLDA-M10-21T_ALL cDNA042110 >>> PlateID >>> Assay Type Absolute Quantification >>> Run DateTime 4/21/10 1:28:40 PM >>> >>> I don't have a copy of the RQ manager software myself, but I know it is >>> on the computer running the machine. I'll see about getting a copy of >>> it for myself or getting some time to do the conversion on the original >>> computer and see about importing the data using HTqPCR::readCtData then. >>> >> Hello Brian, >> >> ExpressionSet objects (and the packages that use them) are specifically >> designed for microarray data. So if you have qPCR data you're better of >> using HTqPCR or some other package designed for qPCR. >> >> It looks like you have standard SDS format. In that case you don't >> need to >> do any conversions to read the data into HTqPCR. If you have the latest >> version, 1.1.4, there's a parameter called "SDS" in readCtData. If you >> set >> that to TRUE it should work. > Hi guys > > I would check and make sure you have a Ct column in the data. Some SDS > export settings will produce it (i.e., the plate-centric view) and some > won't in favor of ddCt and RQ. The header data shows up in them all. > > Mike My files do have a Ct column, so that is promising. I had seen the SDS flag in readCtData, but it did not work even with that. However, I now realize that I have version 1.0 of HTqPCR, probably because I am still on (the as of today no longer current) R 2.10.1 and Bioconductor 2.5. I'm going to wait for the new R 2.11.0 binaries to propagate to my local mirror and for the release of Bioconductor 2.6 (which I understand happens a few days after a release of R) so that I don't have switch to the development versions just to get the latest HTqPCR. I'll see if I can import the data directly without any further manipulations after the update. Thank you both for your help. >> >> HTH >> \Heidi >> >>>>> >>>>> HTH >>>>> \Heidi >>>>>> >>>>>> >>>>>> >>>>>> Though I have used R for a few years, I am starting a project where >>>>>> this >>>>>> is my first real use of Bioconductor and I am having a problem >>>>>> reading >>>>>> expression data from files. The files are created by an Applied >>>>>> Biosystems 7900HT machine. I found the ABarray package, but that only >>>>>> claims to work with AB1700 data. On a lark, I tried to use it for my >>>>>> data, but got an error >>>>>> >>>>>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, >>>>>> na.strings, : >>>>>> line 2 did not have 3 elements >>>>>> >>>>>> which seems consistent with a file not being in the right format. Can >>>>>> anyone tell me if there exists a package that can read this data into >>>>>> an >>>>>> ExpressionSet? Or has anyone even used Bioconductor with data from >>>>>> this, and, if so, what needs to be done to import the data? >>>>>> >>>>>> -- >>>>>> Brian Diggs >>>>>> Senior Research Associate, Department of Surgery, Oregon Health & >>>>>> Science University >>>>>> >>>> >>>> Michael Muratet, Ph.D. >>>> Senior Scientist >>>> HudsonAlpha Institute for Biotechnology >>>> mmuratet-Sy0TgEBENMiWTJ9x5QRIJA-XMD5yJDbdMReXY1tMh2IBg at public.gmane.org >>>> (256) 327-0473 (p) >>>> (256) 327-0966 (f) >>>> >>>> Room 4005 >>>> 601 Genome Way >>>> Huntsville, Alabama 35806 >>>> >>> >>> -- >>> Brian Diggs >>> Senior Research Associate, Department of Surgery, Oregon Health & >>> Science University >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7 at public.gmane.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7 at public.gmane.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > mmuratet-Sy0TgEBENMiWTJ9x5QRIJA at public.gmane.org > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > _______________________________________________ > Bioconductor mailing list > Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7 at public.gmane.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Brian Diggs Senior Research Associate, Department of Surgery, Oregon Health & Science University
ADD REPLYlink written 8.9 years ago by Brian Diggs30
Greetings I have just upgraded R to 2.11, Bioconductor to 2.6 and HTqPCR to 1.2. I am working with data from mouse miRNA experiments on the 7900HT using what I believe are stock ABI cards. Each experimental treatment consists of two distinct cards and there are four treatments for a total of four pairs. There are 4 common controls on each member of the pair (MammU6) but they are otherwise unique. All of the features on the first card are unique (except for the MammU6 control) and the second card has a couple of hundred features in duplicate and a four or so controls repeated four times. What would be the best way to create the qPCRset object? I have tried to concatenate the files by hand and read them in with read.delim and create the qPCRset object by hand. I have tried readCtData(...,SDS=TRUE,sample=c("sample_label")) and combined the two qPCRset objects with rbind() and four samples with cbind(). I have tried to read all the samples in one file. At some point, each one of these approaches fails in the downstream processing. Before I start posting error messages, I thought I would see if anyone has any recommendations. Any suggestions will be welcomed. Thanks Mike Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806
ADD REPLYlink written 8.9 years ago by Michael Muratet420
Hello Michael, I haven't tried working with data spanning multiple cards, but my $0.02 are: - Combining files by hand (either pairwise or all together): Wouldn't be my favourite method, since it involves manual work (*shudder*) - Combining qPCRsets with rbind and cbind: Probably a better option, since you don't necessarily want to normalise the two different types of ABI cards together, but rather do it in two batches before combining them. Depends on the data I guess. Either way, if any of this fails in the downstream process, then feel free to send your code + error messages to the list. Whatever bugs are creeping around in HTqPCR, I need to fix them! HTH \Heidi > Greetings > > I have just upgraded R to 2.11, Bioconductor to 2.6 and HTqPCR to 1.2. > > I am working with data from mouse miRNA experiments on the 7900HT > using what I believe are stock ABI cards. Each experimental treatment > consists of two distinct cards and there are four treatments for a > total of four pairs. There are 4 common controls on each member of the > pair (MammU6) but they are otherwise unique. All of the features on > the first card are unique (except for the MammU6 control) and the > second card has a couple of hundred features in duplicate and a four > or so controls repeated four times. > > What would be the best way to create the qPCRset object? I have tried > to concatenate the files by hand and read them in with read.delim and > create the qPCRset object by hand. I have tried > readCtData(...,SDS=TRUE,sample=c("sample_label")) and combined the two > qPCRset objects with rbind() and four samples with cbind(). I have > tried to read all the samples in one file. At some point, each one of > these approaches fails in the downstream processing. Before I start > posting error messages, I thought I would see if anyone has any > recommendations. > > Any suggestions will be welcomed. > > Thanks > > Mike > > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > mmuratet at hudsonalpha.org > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > > > >
ADD REPLYlink written 8.9 years ago by Heidi Dvinge2.0k
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