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Question: R command readIllumina with beadarray
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gravatar for Hajar Hassani Lahsinoui
6.9 years ago by
Hajar Hassani Lahsinoui120 wrote:
Hi everyone, I practiced using "Analysing Illumina bead-based data using beadarray by Richie & Dunning with the SAMExample dataset. However, when exploring my own beadarraydata I found that my raw data files are txt files and not csv (as they were in the practical). I was able to read the metrics.txt file (this file gives me the date of analysis, beadchip, section...etc), but when I try to use: BLData = readIllumina(arrayNames = metrics$arrayID, textType = ".txt", metrics = metrics, backgroundMethod = "none") I get this response: Found 0 arrays Error in seq.default(1, length(tmp), by = 3) : wrong sign in 'by' argument I've tried replacing arrayID with Beadchip, since it is used in the metrics file, and still it gives me the same message. There should be 24 arrays. Is there another function to read the arrays in R? Thank you in advance, Hajar [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.9 years ago by Matthew Ritchie630 • written 6.9 years ago by Hajar Hassani Lahsinoui120
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gravatar for Tim Triche
6.9 years ago by
Tim Triche4.2k
United States
Tim Triche4.2k wrote:
You could try using BeadDataPackR and summarizing the data yourself if you wish :-) If you are not planning on using BASH or HULK this may actually suit you well. On Sun, Oct 3, 2010 at 10:29 AM, Hajar Hassani Lahsinoui < hajar.hassani@gmail.com> wrote: > Hi everyone, > > I practiced using "Analysing Illumina bead-based data using beadarray by > Richie & Dunning with the SAMExample dataset. However, when exploring my own > beadarraydata I found that my raw data files are txt files and not csv (as > they were in the practical). > I was able to read the metrics.txt file (this file gives me the date of > analysis, beadchip, section...etc), but when I try to use: > > BLData = readIllumina(arrayNames = metrics$arrayID, textType = ".txt", > metrics = metrics, backgroundMethod = "none") > > I get this response: > Found 0 arrays > Error in seq.default(1, length(tmp), by = 3) : wrong sign in 'by' argument > > I've tried replacing arrayID with Beadchip, since it is used in the metrics > file, and still it gives me the same message. There should be 24 arrays. Is > there another function to read the arrays in R? > > Thank you in advance, > > Hajar > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- With four parameters I can fit an elephant, and with five I can make him wiggle his trunk. John von Neumann [[alternative HTML version deleted]]
ADD COMMENTlink written 6.9 years ago by Tim Triche4.2k
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gravatar for Matthew Ritchie
6.9 years ago by
Australia
Matthew Ritchie630 wrote:
Dear Hajar, If this is the same data you mailed the list about the other day, make sure the 'arrayNames' you are specifying are the full names (probably something like '5513091009_A_1_perBeadFile.txt', '5513091009_A_2_perBeadFile.txt' for your first sample if you have WG-6 BeadChips, etc.) Also make sure that all of these files are available in the current working directory - you can check this with dir(pattern="*perBeadFile.txt") If they aren't, change the working directory using the setwd() function. Best wishes, Matt > Hi everyone, > > I practiced using "Analysing Illumina bead-based data using beadarray by > Richie & Dunning with the SAMExample dataset. However, when exploring my > own beadarraydata I found that my raw data files are txt files and not csv > (as they were in the practical). > I was able to read the metrics.txt file (this file gives me the date of > analysis, beadchip, section...etc), but when I try to use: > > BLData = readIllumina(arrayNames = metrics$arrayID, textType = ".txt", > metrics = metrics, backgroundMethod = "none") > > I get this response: > Found 0 arrays > Error in seq.default(1, length(tmp), by = 3) : wrong sign in 'by' argument > > I've tried replacing arrayID with Beadchip, since it is used in the > metrics file, and still it gives me the same message. There should be 24 > arrays. Is there another function to read the arrays in R? > > Thank you in advance, > > Hajar > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 6.9 years ago by Matthew Ritchie630
Thank you Matt!! That helps! Hajar On Oct 4, 2010, at 1:29 AM, Matthew Ritchie wrote: > Dear Hajar, > > If this is the same data you mailed the list about the other day, make > sure the 'arrayNames' you are specifying are the full names (probably > something like '5513091009_A_1_perBeadFile.txt', > '5513091009_A_2_perBeadFile.txt' for your first sample if you have WG-6 > BeadChips, etc.) > > Also make sure that all of these files are available in the current > working directory - you can check this with > > dir(pattern="*perBeadFile.txt") > > If they aren't, change the working directory using the setwd() function. > > Best wishes, > > Matt > >> Hi everyone, >> >> I practiced using "Analysing Illumina bead-based data using beadarray by >> Richie & Dunning with the SAMExample dataset. However, when exploring my >> own beadarraydata I found that my raw data files are txt files and not csv >> (as they were in the practical). >> I was able to read the metrics.txt file (this file gives me the date of >> analysis, beadchip, section...etc), but when I try to use: >> >> BLData = readIllumina(arrayNames = metrics$arrayID, textType = ".txt", >> metrics = metrics, backgroundMethod = "none") >> >> I get this response: >> Found 0 arrays >> Error in seq.default(1, length(tmp), by = 3) : wrong sign in 'by' argument >> >> I've tried replacing arrayID with Beadchip, since it is used in the >> metrics file, and still it gives me the same message. There should be 24 >> arrays. Is there another function to read the arrays in R? >> >> Thank you in advance, >> >> Hajar >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:6}}
ADD REPLYlink written 6.9 years ago by Hajar Hassani Lahsinoui120
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