Importing SMD data

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Georgia Chan ▴ 30

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ADD COMMENT • link 19.2 years ago Georgia Chan ▴ 30

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Georgia Chan ▴ 30

@georgia-chan-1410

Last seen 10.2 years ago

Hi all, I am a newbie to R and BioConductor and (at the moment :) have trouble importing SMD data to R, using read.SMD/read.SMD2 In the working directory, I have 2 files: "14037.xls" with data for one array and its corresponding GAL file "14037.gal", produced by SMD. Below is the debug info from R. Mant thanks in advance, georgia ---------------------------------------------- Output: ---------------------------------------------- > fnames [1] "14037.xls" > read.SMD(fnames=fnames, path=path, DEBUG=TRUE) [1] "14037.xls" Generating layout from 14037.xls [1] "Reading Gal file" Error in "[.data.frame"(dat, , info.id) : undefined columns selected > read.SMD2(fnames=fnames, DEBUG=TRUE) Generating layout from 14037.xls Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed > readLines("14037.gal",30) [1] "ATF\t1.0" [2] "20\t5" [3] "\"Type=GenePix ArrayList V1.0\"" [4] "\"BlockCount=16\"" [5] "\"BlockType=0\"" [6] "\"Block1= 400, 400, 100, 19, 225, 19, 225\"" [7] "\"Block2= 4896, 400, 100, 19, 225, 19, 225\"" [8] "\"Block3= 9392, 400, 100, 19, 225, 19, 225\"" [9] "\"Block4= 13888, 400, 100, 19, 225, 19, 225\"" [10] "\"Block5= 400, 4896, 100, 19, 225, 19, 225\"" [11] "\"Block6= 4896, 4896, 100, 19, 225, 19, 225\"" [12] "\"Block7= 9392, 4896, 100, 19, 225, 19, 225\"" [13] "\"Block8= 13888, 4896, 100, 19, 225, 19, 225\"" [14] "\"Block9= 400, 9392, 100, 19, 225, 19, 225\"" [15] "\"Block10= 4896, 9392, 100, 19, 225, 19, 225\""

ADD COMMENT • link 19.2 years ago Georgia Chan ▴ 30

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Hi, Georgia - At a guess, your .xls file from SMD is in an old format. The current version of read.SMD expects column headers such as "Ch1 Intensity (Median)." If you instead have headers like "CH1I_MEDIAN," I don't think read.SMD will handle it. If this is the case, you should be able to use read.maimages() from the limma package, with source="smd.old". You could then use the convert package from BioConductor to make appropriate marray objects from the limma object(s). Hope this helps - -- Jeremy Gollub, Ph.D. jgollub at genome.stanford.edu (W) 650/736-0075 On Tue, 6 Sep 2005, Georgia Chan wrote: > Hi all, > I am a newbie to R and BioConductor and > (at the moment :) have trouble importing > SMD data to R, using read.SMD/read.SMD2 > > In the working directory, I have 2 files: > "14037.xls" with data for one array and > its corresponding GAL file "14037.gal", > produced by SMD. > > Below is the debug info from R. > > Mant thanks in advance, > georgia > > > ---------------------------------------------- > Output: > ---------------------------------------------- > > fnames > [1] "14037.xls" > > > read.SMD(fnames=fnames, path=path, DEBUG=TRUE) > [1] "14037.xls" > Generating layout from 14037.xls > [1] "Reading Gal file" > Error in "[.data.frame"(dat, , info.id) : undefined columns selected > > > read.SMD2(fnames=fnames, DEBUG=TRUE) > Generating layout from 14037.xls > Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed > > > readLines("14037.gal",30) > [1] "ATF\t1.0" > [2] "20\t5" > [3] "\"Type=GenePix ArrayList V1.0\"" > [4] "\"BlockCount=16\"" > [5] "\"BlockType=0\"" > [6] "\"Block1= 400, 400, 100, 19, 225, 19, 225\"" > [7] "\"Block2= 4896, 400, 100, 19, 225, 19, 225\"" > [8] "\"Block3= 9392, 400, 100, 19, 225, 19, 225\"" > [9] "\"Block4= 13888, 400, 100, 19, 225, 19, 225\"" > [10] "\"Block5= 400, 4896, 100, 19, 225, 19, 225\"" > [11] "\"Block6= 4896, 4896, 100, 19, 225, 19, 225\"" > [12] "\"Block7= 9392, 4896, 100, 19, 225, 19, 225\"" > [13] "\"Block8= 13888, 4896, 100, 19, 225, 19, 225\"" > [14] "\"Block9= 400, 9392, 100, 19, 225, 19, 225\"" > [15] "\"Block10= 4896, 9392, 100, 19, 225, 19, 225\"" > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

ADD REPLY • link 19.2 years ago Jeremy Gollub ▴ 80

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Maria Persico ▴ 100

@maria-persico-1072

Last seen 10.2 years ago

Hello, I'm using GraphAT package to "measure" the congruency between an experimental dataset and the metadata GO biological process. my experimental dataset is small if compared with GO meta data. The specie on which I'm working is Yeast(cerevisiae). The important absumption with the method "getpvalue" of GraphAT package is that the graphs that you want "compare" must have the same nodes(obviously the number of edges should be different). If the 2 adj matrices you want compare are different in size you get an error. In my specific case, I created a subset of the big GO meta data file(in this subset I had only the nodes that were present in the experimental dataset) and I tried to remove from this subset only the edges that gave as similarity measures, values of Dij<3.I had 109 edges of this kind. So I did : for(i in 1:109){ GgoPredYBPnew<-removeEdge(as.character(edges.to.delete$V1[i]), as.character(edges.to.delete$V2[i]), GgoPredYBP) } but the graph that I obtained was only of one edge smaller!!! May somebody help me? I would have also some other questions regarding this package: how to use the information about the edge weights? for example I want to consider as "common edges" between two graph only the ones that have a certain values in their edge weights.... If the graphs that I want to compare have a different set of nodes (some in common ), does some method could be developed to work directly only with nodes in common? thanks for your attention. maria Maria Persico MINT database, Cesareni Group Universita' di Tor Vergata, via della Ricerca Scientifica 00133 Roma, Italy Tel: +39 0672594315 FAX: +39 0672594766 e-mail: maria at cbm.bio.uniroma2.it

ADD COMMENT • link 19.2 years ago Maria Persico ▴ 100

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