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Question: incomplete final row of every block
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13.6 years ago by
Mark Robinson10 wrote:
Hi. We have these homemade arrays that have nothing printed in the last 9 columns of the last row of each grid. 4x4 grids, 21x21 spots in each grid == 7056 possible of which we have only 6912 and 9*16 as empty. So, the data files have 6913 lines (one for header). I'm new to Bioconductor and am having trouble getting it to do a Loess normalization. Here is what I have: # make gene lists, sample lists my.targets<-read.marrayInfo("mySamples.txt") my.gnames<-read.marrayInfo("layout.txt",info.id=2,label=2,skip=1) # make layout layout<-read.table("layout.txt",sep="\t",header=T) my.layout<-read.marrayLayout(ngr=4,ngc=4,nsr=21,nsc=21) maSub(my.layout)<-layout$Control!="control" control<-rep(0,dim(layout)[1]) control[grep("TH",as.character(layout$Gene))]<-1 maControls(my.layout)<-as.logical(control) # read in data my.oe<-read.marrayRaw(as.character(my.targets@maInfo$Names), name.Gf="F532 Location",name.Gb="B532 Location", name.Rf="F635 Location",name.Rb="B635 Location", gnames=my.gnames,layout=my.layout,targets=my.targets) # median normalize. my.norm<-maNormMain(my.oe,f.loc=list(maNormLoess())) --This last line gets the following error: > my.norm<-maNormMain(my.oe,f.loc=list(maNormLoess())) Error: dim<- : dims [product 6307] do not match the length of object [6439] In addition: Warning message: longer object length is not a multiple of shorter object length in: samplesub & which & subset & good --Also, I get an error from the following: maGeneTable(my.oe) > maGeneTable(my.oe) Error in data.frame(GR = maGridRow(object), GC = maGridCol(object), SR = maSpotRow(object), : arguments imply differing number of rows: 6439, 6912 I'm not surprised by the errors, I'm just not exactly sure how to input the data in the correct way ... well, without adding dummy lines into my data file and layout file. Is there an easier way? layout.txt looks like: ... 92 YDL107W 1 5 8 probe 93 YDL109C 1 5 9 probe 94 YDL199C 1 5 10 probe ... Thanks, Mark -- ADD COMMENTlink modified 13.6 years ago by Jean Yee Hwa Yang920 • written 13.6 years ago by Mark Robinson10 0 13.6 years ago by Jean Yee Hwa Yang920 wrote: Hi Mark, If you were trying out median normalization, try maNorm(my.oe, norm="m") How many lines do you have in the layout file? In order for print-tip loess to work on your array, you will need to set up my.layout@maSub properly. This should be a logical vector of length 7056. For the corresponding position of 9 * 16 = 144 empty spots (that are not in the data file), the value should be set to "FALSE". Cheers Jean As for setting up the layout, I assume the control columns in > > control<-rep(0,dim(layout)[1]) > control[grep("TH",as.character(layout$Gene))]<-1 > maControls(my.layout)<-as.logical(control) > > # read in data > my.oe<-read.marrayRaw(as.character(my.targets@maInfo\$Names), > name.Gf="F532 Location",name.Gb="B532 Location", > name.Rf="F635 Location",name.Rb="B635 Location", > gnames=my.gnames,layout=my.layout,targets=my.targets) > > # median normalize. > my.norm<-maNormMain(my.oe,f.loc=list(maNormLoess()))