Beadarray expression data
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Ina Hoeschele ▴ 110
@ina-hoeschele-2310
Last seen 10.2 years ago
Hi all, I am completely new to the analysis of Illumina Beadarray gene expression data (but quite familiar with Affy data). Such data (with samples run on 3 chips) was sent to me by a collaborator. From the vignettes for Bioconductor packages 'beadarray' and 'BeadExplorer', it looks like these accommodate Beadstudio version 1 and 2 data, while our data was created by BeadStudio version 3.0.14.. Would it still work? My collaborator sent two types of files to me: (1) a number of .csv files (read by excel, 2 for each sample) with columns Illumicode, N, mean GRN, Dev GRN. (2) a summary .txt file with columns TargetID MIN_Signal-1814647013_A AVG_Signal-1814647013_A MAX_Signal-1814647013_A NARRAYS-1814647013_A ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A Avg_NBEADS-1814647013_A Detection-1814647013_A, with the MIN_Signal-... to Detection-... columns repeated for the remaining samples. It looks like beadarray expects to read the summary data from a .csv rather than a .txt file? From the example given on page 2 of the beadarray vignette, the summary data are read in by BSData <- readBeadSummaryData(datafile, ..., columns = list(exprs = AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS", ...) Since I have AVG_Signal-1814647013_A, AVG_Signal-1814647013_B etc. and not just one AVG_Signal, how do I specify the columns to be read? Sorry for these ignorant questions, but this is my first try at these data. Thanks for any advice! Ina
affy beadarray affy beadarray • 1.6k views
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Simon Luo ▴ 10
@simon-luo-2311
Last seen 10.2 years ago
Ina Hoeschele <inah at="" ...=""> writes: > > Hi all, > I am completely new to the analysis of Illumina Beadarray gene > expression data (but quite familiar with Affy data). Such data (with > samples run on 3 chips) was sent to me by a collaborator. From the > vignettes for Bioconductor packages 'beadarray' and 'BeadExplorer', it > looks like these accommodate Beadstudio version 1 and 2 data, while our > data was created by BeadStudio version 3.0.14.. Would it still work? My > collaborator sent two types of files to me: (1) a number of .csv files > (read by excel, 2 for each sample) with columns Illumicode, N, mean GRN, > Dev GRN. (2) a summary .txt file with columns TargetID > MIN_Signal-1814647013_A AVG_Signal-1814647013_A > MAX_Signal-1814647013_A NARRAYS-1814647013_A > ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A > Avg_NBEADS-1814647013_A Detection-1814647013_A, with the > MIN_Signal-... to Detection-... columns repeated for the remaining samples. > It looks like beadarray expects to read the summary data from a .csv > rather than a .txt file? From the example given on page 2 of the > beadarray vignette, the summary data are read in by > BSData <- readBeadSummaryData(datafile, ..., columns = list(exprs = > AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS", ...) > > Since I have AVG_Signal-1814647013_A, AVG_Signal-1814647013_B etc. and > not just one AVG_Signal, how do I specify the columns to be read? > > Sorry for these ignorant questions, but this is my first try at these > data. Thanks for any advice! > Ina > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi Ina, I used beadarray version 1.2.2 and my bead summary data were from BeadStudio V2. I don't think the BeadStudio version should not be a concern when extracting the bead summary data from the raw data file (either .txt or csv file). Your data are summary data because of the column "AVG_Signal-", readBeadSummaryData() function reads in all the columns begin with "AVG_Signal-" from the summary data file and create a BSData object for further preprocessing steps. If you still concern about the version compatibility, you can use something like read.table/read.csv to extract the raw summary data (all columns start with "AVG_Signal-") and compare the result to the BSData object that you obtained from using readBeadSummaryData() function. Regarding how to use the readBeadSummaryData() function in beadarray, if you set everything correct in the target file, in which you need to name the path of your raw data file and other information for the data set (refer to beadarray vignette for details), you don't need to pass anything for the parameter columns. The function knows what to do with the columns in the data file. Best, Simon
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Hello Simon If you are using beadarray package, you first have to read the data file into an object, like this data<-read.csv("data_file.csv", skip=7) You have got to skip the first 7 rows as these just contain general information. To select a set of columns which is required for the analysis step, you can use the function subset. Expression <- subset(data, select = grep("AVG", names(data))) The above line selets all the columns starting with their names as AVG Beads <- subset(data, select = grep("Avg", names(data))) This selects all columns that start with Avg Hope this helps? Yogi _____ Yoganand Sundaravadanam Bioinformatics Officer Australian Genome Research Facility Ltd Level 5 Gehrmann Laboratories Research Road University of Queensland St Lucia QLD Phone: +61 7 3346 7328 Fax: +61 7 3365 1823 Email: yogi.sundaravadanam at agrf.org.au Web: www.agrf.org.au Subscribe to the AGRF Newsletter _____ Please Note: The message is intended only for the addressee. If you receive this message in error please do not publish, distribute, or copy it. Please advise the AGRF by telephone or email, and delete this message from your computer. -----Original Message----- From: simonlaw23@hotmail.com [mailto:simonlaw23@hotmail.com] Sent: Wednesday, 8 August 2007 7:28 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Beadarray expression data Ina Hoeschele <inah at="" ...=""> writes: > > Hi all, > I am completely new to the analysis of Illumina Beadarray gene > expression data (but quite familiar with Affy data). Such data (with > samples run on 3 chips) was sent to me by a collaborator. From the > vignettes for Bioconductor packages 'beadarray' and 'BeadExplorer', it > looks like these accommodate Beadstudio version 1 and 2 data, while our > data was created by BeadStudio version 3.0.14.. Would it still work? My > collaborator sent two types of files to me: (1) a number of .csv files > (read by excel, 2 for each sample) with columns Illumicode, N, mean GRN, > Dev GRN. (2) a summary .txt file with columns TargetID > MIN_Signal-1814647013_A AVG_Signal-1814647013_A > MAX_Signal-1814647013_A NARRAYS-1814647013_A > ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A > Avg_NBEADS-1814647013_A Detection-1814647013_A, with the > MIN_Signal-... to Detection-... columns repeated for the remaining samples. > It looks like beadarray expects to read the summary data from a .csv > rather than a .txt file? From the example given on page 2 of the > beadarray vignette, the summary data are read in by > BSData <- readBeadSummaryData(datafile, ..., columns = list(exprs = > AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS", ...) > > Since I have AVG_Signal-1814647013_A, AVG_Signal-1814647013_B etc. and > not just one AVG_Signal, how do I specify the columns to be read? > > Sorry for these ignorant questions, but this is my first try at these > data. Thanks for any advice! > Ina > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi Ina, I used beadarray version 1.2.2 and my bead summary data were from BeadStudio V2. I don't think the BeadStudio version should not be a concern when extracting the bead summary data from the raw data file (either .txt or csv file). Your data are summary data because of the column "AVG_Signal-", readBeadSummaryData() function reads in all the columns begin with "AVG_Signal-" from the summary data file and create a BSData object for further preprocessing steps. If you still concern about the version compatibility, you can use something like read.table/read.csv to extract the raw summary data (all columns start with "AVG_Signal-") and compare the result to the BSData object that you obtained from using readBeadSummaryData() function. Regarding how to use the readBeadSummaryData() function in beadarray, if you set everything correct in the target file, in which you need to name the path of your raw data file and other information for the data set (refer to beadarray vignette for details), you don't need to pass anything for the parameter columns. The function knows what to do with the columns in the data file. Best, Simon _______________________________________________ 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
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Sorry Simon, that was meant for Ina Cheers _____ Yoganand Sundaravadanam Bioinformatics Officer Australian Genome Research Facility Ltd Level 5 Gehrmann Laboratories Research Road University of Queensland St Lucia QLD Phone: +61 7 3346 7328 Fax: +61 7 3365 1823 Email: yogi.sundaravadanam at agrf.org.au Web: www.agrf.org.au Subscribe to the AGRF Newsletter _____ Please Note: The message is intended only for the addressee. If you receive this message in error please do not publish, distribute, or copy it. Please advise the AGRF by telephone or email, and delete this message from your computer. -----Original Message----- From: Yogi Sundaravadanam Sent: Wednesday, 8 August 2007 9:07 AM To: bioconductor; simonlaw23 Subject: Re: [BioC] Beadarray expression data Hello Simon If you are using beadarray package, you first have to read the data file into an object, like this data<-read.csv("data_file.csv", skip=7) You have got to skip the first 7 rows as these just contain general information. To select a set of columns which is required for the analysis step, you can use the function subset. Expression <- subset(data, select = grep("AVG", names(data))) The above line selets all the columns starting with their names as AVG Beads <- subset(data, select = grep("Avg", names(data))) This selects all columns that start with Avg Hope this helps? Yogi _____ Yoganand Sundaravadanam Bioinformatics Officer Australian Genome Research Facility Ltd Level 5 Gehrmann Laboratories Research Road University of Queensland St Lucia QLD Phone: +61 7 3346 7328 Fax: +61 7 3365 1823 Email: yogi.sundaravadanam at agrf.org.au Web: www.agrf.org.au Subscribe to the AGRF Newsletter _____ Please Note: The message is intended only for the addressee. If you receive this message in error please do not publish, distribute, or copy it. Please advise the AGRF by telephone or email, and delete this message from your computer. -----Original Message----- From: simonlaw23@hotmail.com [mailto:simonlaw23@hotmail.com] Sent: Wednesday, 8 August 2007 7:28 AM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Beadarray expression data Ina Hoeschele <inah at="" ...=""> writes: > > Hi all, > I am completely new to the analysis of Illumina Beadarray gene > expression data (but quite familiar with Affy data). Such data (with > samples run on 3 chips) was sent to me by a collaborator. From the > vignettes for Bioconductor packages 'beadarray' and 'BeadExplorer', it > looks like these accommodate Beadstudio version 1 and 2 data, while our > data was created by BeadStudio version 3.0.14.. Would it still work? My > collaborator sent two types of files to me: (1) a number of .csv files > (read by excel, 2 for each sample) with columns Illumicode, N, mean GRN, > Dev GRN. (2) a summary .txt file with columns TargetID > MIN_Signal-1814647013_A AVG_Signal-1814647013_A > MAX_Signal-1814647013_A NARRAYS-1814647013_A > ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A > Avg_NBEADS-1814647013_A Detection-1814647013_A, with the > MIN_Signal-... to Detection-... columns repeated for the remaining samples. > It looks like beadarray expects to read the summary data from a .csv > rather than a .txt file? From the example given on page 2 of the > beadarray vignette, the summary data are read in by > BSData <- readBeadSummaryData(datafile, ..., columns = list(exprs = > AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS", ...) > > Since I have AVG_Signal-1814647013_A, AVG_Signal-1814647013_B etc. and > not just one AVG_Signal, how do I specify the columns to be read? > > Sorry for these ignorant questions, but this is my first try at these > data. Thanks for any advice! > Ina > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi Ina, I used beadarray version 1.2.2 and my bead summary data were from BeadStudio V2. I don't think the BeadStudio version should not be a concern when extracting the bead summary data from the raw data file (either .txt or csv file). Your data are summary data because of the column "AVG_Signal-", readBeadSummaryData() function reads in all the columns begin with "AVG_Signal-" from the summary data file and create a BSData object for further preprocessing steps. If you still concern about the version compatibility, you can use something like read.table/read.csv to extract the raw summary data (all columns start with "AVG_Signal-") and compare the result to the BSData object that you obtained from using readBeadSummaryData() function. Regarding how to use the readBeadSummaryData() function in beadarray, if you set everything correct in the target file, in which you need to name the path of your raw data file and other information for the data set (refer to beadarray vignette for details), you don't need to pass anything for the parameter columns. The function knows what to do with the columns in the data file. Best, Simon _______________________________________________ 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
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Mark Dunning ▴ 320
@mark-dunning-1634
Last seen 10.2 years ago
Hi, The beadarray package can read the output from BeadStudio version 3. In fact all you need to do is change the skip parameter so that it ignores the first 8 lines of output from BeadStudio 3 , which are all header information The following function call should do the trick. B = readBeadSummaryData(dataFile, skip=8, sep="\t") When specifying the column names to read, you just need to specify the expression values are found in columns with the prefix "AVG_Signal". The function then searches through the column names and finds all instances of this string and creates an matrix with the appropriate number of columns. Hope this helps, Mark On 7 Aug 2007, at 21:14, Ina Hoeschele wrote: > Hi all, > I am completely new to the analysis of Illumina Beadarray gene > expression data (but quite familiar with Affy data). Such data (with > samples run on 3 chips) was sent to me by a collaborator. From the > vignettes for Bioconductor packages 'beadarray' and 'BeadExplorer', it > looks like these accommodate Beadstudio version 1 and 2 data, > while our > data was created by BeadStudio version 3.0.14.. Would it still > work? My > collaborator sent two types of files to me: (1) a number of .csv files > (read by excel, 2 for each sample) with columns Illumicode, N, mean > GRN, > Dev GRN. (2) a summary .txt file with columns TargetID > MIN_Signal-1814647013_A AVG_Signal-1814647013_A > MAX_Signal-1814647013_A NARRAYS-1814647013_A > ARRAY_STDEV-1814647013_A BEAD_STDEV-1814647013_A > Avg_NBEADS-1814647013_A Detection-1814647013_A, with the > MIN_Signal-... to Detection-... columns repeated for the remaining > samples. > It looks like beadarray expects to read the summary data from a .csv > rather than a .txt file? From the example given on page 2 of the > beadarray vignette, the summary data are read in by > BSData <- readBeadSummaryData(datafile, ..., columns = list(exprs = > AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS", ...) > > Since I have AVG_Signal-1814647013_A, AVG_Signal-1814647013_B etc. and > not just one AVG_Signal, how do I specify the columns to be read? > > Sorry for these ignorant questions, but this is my first try at these > data. Thanks for any advice! > Ina > > _______________________________________________ > 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
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