Reading SMD data in limma
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
Dear Rohit, The problem appears to be that your data files have different numbers of rows. The first 7 files have the same number of rows, but then the 8th file is different. Try this: x1 <- read.maimages(files=filelist[1:7],... x2 <- read.maimages(files=filelist[8],... dim(x1) dim(x2) Best wishes Gordon > Date: Wed, 9 Jun 2010 12:57:33 +0530 > From: Rohit Farmer <rohit.farmer at="" gmail.com=""> > To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Reading SMD data in limma > > Hello everyone ... i am trying to make an object from an SMD data > downloaded from ArrayExpress ... using the limma package and used the > following command .... but getting this error and the object is not being > created .. > > > data <- read.maimages(files=filelist, source="smd", > columns=list(R="ScanAlyze:RESULT.CH1I_MEAN",G="ScanAlyze:RESULT.CH2I _MEAN",Rb="ScanAlyze:RESULT.CH1B_MEDIAN",Gb="ScanAlyze:RESULT.CH2B_MED IAN")) > Read E-SMDB-1428-raw-data-516957410.txt > Read E-SMDB-1428-raw-data-516957425.txt > Read E-SMDB-1428-raw-data-516957442.txt > Read E-SMDB-1428-raw-data-516957457.txt > Read E-SMDB-1428-raw-data-516957472.txt > Read E-SMDB-1428-raw-data-516957490.txt > Read E-SMDB-1428-raw-data-516957507.txt > Error in RG[[a]][, i] <- obj[, columns[[a]]] : > number of items to replace is not a multiple of replacement length > > > Please help to sort this problem > > Regard > rohit > -- > Rohit Farmer > M.Tech Bioinformatics > Department of Computational Biology and Bioinformatics > Jacob School of Biengineering and Biotechnology > Sam Higginbottom Institute of Agriculture, Technology and Sciences > (Formerly known as Allahabad Agricultural Institute - Deemed University) > Allahabad, UP, INDIA - 211 007 > Ph. No. 9839845093, 9415261403 > e-Mail rohit.farmer at gmail.com > Blog http://rohitsspace.blogspot.com ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
limma ArrayExpress limma ArrayExpress • 530 views
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@audrey-kauffmann-3982
Last seen 6.6 years ago
Dear Rohit, Regarding your first question about the use of the ArrayExpress package, the error message indicated to try to set the rawcol argument using the names listed. For instance, you could try: > data = ArrayExpress("E-SMDB-1428", rawcol = list(R="ScanAlyze:RESULT.CH2I_MEAN", G"ScanAlyze:RESULT.CH1I_MEAN", Rb="ScanAlyze:RESULT.CH2B_MEDIAN", Gb="ScanAlyze:RESULT.CH1B_MEDIAN")) The output is a list of two NChannelSet because one of the file has a different format as Gordon mentionned. Best wishes, Audrey 2010/6/10 Gordon K Smyth <smyth at="" wehi.edu.au="">: > Dear Rohit, > > The problem appears to be that your data files have different numbers of > rows. ?The first 7 files have the same number of rows, but then the 8th file > is different. ?Try this: > > ?x1 <- read.maimages(files=filelist[1:7],... > ?x2 <- read.maimages(files=filelist[8],... > > ?dim(x1) > ?dim(x2) > > Best wishes > Gordon > >> Date: Wed, 9 Jun 2010 12:57:33 +0530 >> From: Rohit Farmer <rohit.farmer at="" gmail.com=""> >> To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> >> Subject: [BioC] Reading SMD data in limma >> >> Hello everyone ... i am trying to make an object from an SMD data >> downloaded ?from ArrayExpress ... using the limma package and used the >> following command .... but getting this error and the object is not being >> created .. >> >> >> data <- read.maimages(files=filelist, source="smd", >> >> columns=list(R="ScanAlyze:RESULT.CH1I_MEAN",G="ScanAlyze:RESULT.CH2 I_MEAN",Rb="ScanAlyze:RESULT.CH1B_MEDIAN",Gb="ScanAlyze:RESULT.CH2B_ME DIAN")) >> Read E-SMDB-1428-raw-data-516957410.txt >> Read E-SMDB-1428-raw-data-516957425.txt >> Read E-SMDB-1428-raw-data-516957442.txt >> Read E-SMDB-1428-raw-data-516957457.txt >> Read E-SMDB-1428-raw-data-516957472.txt >> Read E-SMDB-1428-raw-data-516957490.txt >> Read E-SMDB-1428-raw-data-516957507.txt >> Error in RG[[a]][, i] <- obj[, columns[[a]]] : >> ?number of items to replace is not a multiple of replacement length >> >> >> Please help to sort this problem >> >> Regard >> rohit >> -- >> Rohit Farmer >> M.Tech Bioinformatics >> Department of Computational Biology and Bioinformatics >> Jacob School of Biengineering and Biotechnology >> Sam Higginbottom Institute of Agriculture, Technology and Sciences >> (Formerly known as Allahabad Agricultural Institute - Deemed University) >> Allahabad, UP, INDIA - 211 007 >> Ph. No. 9839845093, 9415261403 >> e-Mail rohit.farmer at gmail.com >> Blog http://rohitsspace.blogspot.com > > ______________________________________________________________________ > The information in this email is confidential and intend...{{dropped:4}} > > _______________________________________________ > 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 > -- Audrey Kauffmann Bergonie Cancer Institute 229 Cours de l'Argonne 33076 Bordeaux France +33.5.56.33.04.53
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
Dear Budhayash, You cannot combine arrays 1-7 with arrays 9-16 unless they have the same probes. So you need to figure out which are the extra probes in arrays 1-7 and remove them (by subsetting the RG object you've read in). Then you can use cbind() to put the first and second groups together. We have no control over what authors put on ArrayExpress, so there is no general solution. It is not possible to give more specific advice, such as code examples, from the information you give. Best wishes Gordon ----------------------------------------------- Associate Professor Gordon K Smyth, NHMRC Senior Research Fellow, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3052, Australia. smyth at wehi.edu.au http://www.wehi.edu.au http://www.statsci.org/smyth > Date: Fri, 18 Jun 2010 16:34:50 +0530 > From: Budhayash Gautam <budhayashgautam at="" gmail.com=""> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Reading SMD data in limma > > Hello everyone ... i am trying to make an object from an SMD data > downloaded from ArrayExpress ... using the limma package .. but getting > this error and the object is not being created ...... number of items to > replace is not a multiple of replacement length. > > The problem appears to be that data files (total 16 files) have > different numbers of rows. All the files have the same number of rows > (5337 rows), but only the 8th file is different (4993 rows). how these > rows can be made similar in number so that all files can be changed to > a single object. > > how can i deal with this situation. if we read files (1-7 & 9-16) and > 8 separately then two objects will be created then how can these two > objects be merged for further analysis. > > Please help to sort this problem > > Regard > > -- > BUDHAYASH ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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