Question: chipAlongChrom problem in Ringo
0
10.9 years ago by
Jianping Jin890
Jianping Jin890 wrote:
Hi list, I ran into a problem using chipAlongChrom to visualize a Chip chip array intensities: > chipAlongChrom(X,chrom="5", probeAnno=probeAnno,gff=mm9genes2, xlim=c(37.63e6, 37.64e6), ylim=c(-3,5), paletteName="S et2") Getting probe intensities in selected regions.., Preparing color scheme... Plotting intensities... Obtain genomic features... Warning messages: 1: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff = mm9genes2, : The identifiers of 28 reporters in the region to plot are not found as 'featureNames' of X 2: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff = mm9genes2, : Only NA values in specified region. A plot came up and could display everything except intensity data which are supposed to center around the dashed zero line. This function uses gff, probeAnno and expression set files. What file(s) should I check, or a script issue? Thanks, Jianping ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu
probe • 623 views
modified 10.9 years ago by Joern Toedling720 • written 10.9 years ago by Jianping Jin890
Answer: chipAlongChrom problem in Ringo
0
10.9 years ago by
Joern Toedling720 wrote:
Hello, are the warning messages any indication what the source of the problem might be? Does the probeAnno object that you use really correspond to the microarray platform of your ExpressionSet "X"? Maybe you accidentally used a probeAnno from another array platform. Are there actually any probes mapping to this region that you wanted to plot. The region is selected by specifying the argument "xlim" as c (<the start="" site="" that="" you="" want="">, <the end="" site="" that="" you="" want="">). Try something like table(probeAnno["5.index"] %in% featureNames(X)) to see how many probes in your probeAnno are actually defined on your array. Try different chromosomes and regions to figure out what is wrong. Potentially you may have to rebuild the probeAnno object for that array. Regards, Joern PS: Please also always provide the output of sessionInfo() when asking questions on this list, so we can figure out if outdated or conflicting versions of certain packages could be a source of problems. Jianping Jin wrote: > Hi list, > > I ran into a problem using chipAlongChrom to visualize a Chip chip > array intensities: > >> chipAlongChrom(X,chrom="5", probeAnno=probeAnno,gff=mm9genes2, > xlim=c(37.63e6, 37.64e6), ylim=c(-3,5), paletteName="S > et2") > Getting probe intensities in selected regions.., > Preparing color scheme... > Plotting intensities... > Obtain genomic features... > Warning messages: > 1: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff = > mm9genes2, : > The identifiers of 28 reporters in the region to plot are not found > as 'featureNames' of X > > 2: In chipAlongChrom(X, chrom = "5", probeAnno = probeAnno, gff = > mm9genes2, : > Only NA values in specified region. > > A plot came up and could display everything except intensity data > which are supposed to center around the dashed zero line. This > function uses gff, probeAnno and expression set files. What file(s) > should I check, or a script issue? > > Thanks, > > Jianping > -- Joern Toedling EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Phone +44(0)1223 492566 Email toedling at ebi.ac.uk
Jianping Jin wrote: > table(probeAnno["5.index"] %in% featureNames(X)) > > FALSE > 21152 well, none of the probes seems to be included in the names of the probes on your arrays. How did you create the object "X"? Can you show me the output of str(probeAnno["5.index"]) str(probeAnno["5.start"]) str(probeAnno["5.end"]) ## and for comparison: str(probeAnno["1.index"]) str(probeAnno["1.start"]) # And what is str(featureNames(X)) featureNames(X)[1:30] str(X) dim(X) > > What are feature names in probeAnno? Actually I used a new output file > from the script you edited to generate probeAnno with no complain: > > probeAnno <- > posToProbeAnno("C:/from_DriveD/Chip- chip/Bultman/allChromExonerateOut_new.txt") > > Creating probeAnno mapping for chromosome 1 10 11 12 13 14 15 16 17 > 18 19 2 3 4 5 6 7 8 9 X Y Done. > allChrs <- chromosomeNames(probeAnno) > genome(probeAnno) <- "M. musculus (mm9)" > arrayName(probeAnno) <- "2007-02-27_MM8_CpG_Island_Pro_Tiling" This looks alright to me. I think the function is working, but somehow the probeAnno does not seem to match your data ExpressionSet. Maybe can you also provide me with the first few lines of this file, just to be sure? C:/from_DriveD/Chip-chip/Bultman/allChromExonerateOut_new.txt Joern
X was created as the following: MAs <- lapply(RGs, function(thisRG) preprocess(thisRG[thisRG$genes$Status=="Probe",], method="nimblegen", returnMAList=TRUE)) MA <- do.call("rbind", MAs) X <- asExprSet(MA) sampleNames(X) <- paste(X$Cy5, X$Feed,sep=".") > str(probeAnno["5.index"]) chr [1:21152] "5313_0084_0040" "5313_0760_0290" "5313_0060_0330" ... > str(probeAnno["5.start"]) int [1:21152] 3000580 3000665 3000780 3000860 3000975 3001082 3001162 3001282 3001362 3001462 ... > str(probeAnno["5.end"]) int [1:21152] 3000638 3000718 3000837 3000909 3001035 3001138 3001215 3001339 3001422 3001523 ... > str(probeAnno["1.index"]) chr [1:20363] "5313_0105_0555" "5313_0211_0843" "5313_0492_0238" ... > str(probeAnno["1.start"]) int [1:20363] 3521489 3521564 3521689 3521764 3521874 3521969 3522064 3522164 3660593 3660683 ... > str(probeAnno["1.end"]) int [1:20363] 3521542 3521613 3521738 3521813 3521923 3522018 3522113 3522213 3660642 3660732 ... > str(featureNames(X)) chr [1:1495582] "MM5000P00314500" "MM5000P00286227" ... > str(featureNames(X)) chr [1:1121049] "CHR10FS100018407" "CHR10FS100018507" ... > featureNames(X)[1:30] [1] "CHR10FS100018407" "CHR10FS100018507" "CHR10FS100018612" "CHR10FS100018717" [5] "CHR10FS100018817" "CHR10FS100018927" "CHR10FS100019007" "CHR10FS100019103" [9] "CHR10FS100019228" "CHR10FS100019328" "CHR10FS100019428" "CHR10FS100019503" [13] "CHR10FS100019603" "CHR10FS100019703" "CHR10FS100019824" "CHR10FS100019927" [17] "CHR10FS100020027" "CHR10FS100020117" "CHR10FS010119532" "CHR10FS010119652" [21] "CHR10FS010119737" "CHR10FS010119840" "CHR10FS010119947" "CHR10FS010120052" [25] "CHR10FS010120142" "CHR10FS010120232" "CHR10FS010120343" "CHR10FS010120453" [29] "CHR10FS010120552" "CHR10FS010120652" > str(X) Formal class 'ExpressionSet' [package "Biobase"] with 6 slots ..@ assayData :<environment: 0x1723efb8=""> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 8 obs. of 2 variables: .. .. .. ..$varLabel : Factor w/ 8 levels "Cy3","Cy5","DESIGN_NAME",..: 8 5 6 3 7 1 2 4 .. .. .. ..$ labelDescription: chr [1:8] NA NA NA NA ... .. .. ..@ data :'data.frame': 2 obs. of 8 variables: .. .. .. ..$SlideNumber : int [1:2] 19657602 20613302 .. .. .. ..$ FileNameCy3 : chr [1:2] "19657602_532.pair" "20613302_532.pair" .. .. .. ..$FileNameCy5 : chr [1:2] "19657602_635.pair" "20613302_635.pair" .. .. .. ..$ DESIGN_NAME : chr [1:2] "2007-02-27_MM8_CpG_Island_Pro" "2007-02-27_MM8_CpG_Island_Pro" .. .. .. ..$SAMPLE_SPECIES: chr [1:2] "B6" "B6" .. .. .. ..$ Cy3 : chr [1:2] "SPF1-input" "GF2-input" .. .. .. ..$Cy5 : chr [1:2] "SPF1-ChIP" "GF1-ChIP" .. .. .. ..$ Feed : chr [1:2] "normFed" "germFree" .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$: int [1:3] 1 1 0 ..@ featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 7 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:7] NA NA NA NA ... .. .. ..@ data :'data.frame': 1121049 obs. of 7 variables: .. .. .. ..$GENE_EXPR_OPTION: Factor w/ 2 levels "BLOCK1","RANDOM": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ PROBE_ID : Factor w/ 389307 levels "CHR01FS003521489",..: 225730 225731 225732 225733 225734 225735 225736 225737 225738 225739 ... .. .. .. ..$POSITION : int [1:1121049] 100018407 100018507 100018612 100018717 100018817 100018927 100019007 100019103 100019228 100019328 ... .. .. .. ..$ X : int [1:1121049] 694 181 365 233 96 314 735 330 640 379 ... .. .. .. ..$Y : int [1:1121049] 524 959 429 425 22 286 487 138 636 11 ... .. .. .. ..$ Status : chr [1:1121049] "Probe" "Probe" "Probe" "Probe" ... .. .. .. ..$ID : chr [1:1121049] "CHR10FS100018407" "CHR10FS100018507" "CHR10FS100018612" "CHR10FS100018717" ... .. .. ..@ dimLabels : chr [1:2] "rowNames" "columnNames" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots .. .. ..@ name : chr "" .. .. ..@ lab : chr "" .. .. ..@ contact : chr "" .. .. ..@ title : chr "" .. .. ..@ abstract : chr "" .. .. ..@ url : chr "" .. .. ..@ pubMedIds : chr "" .. .. ..@ samples : list() .. .. ..@ hybridizations : list() .. .. ..@ normControls : list() .. .. ..@ preprocessing : list() .. .. ..@ other : list() .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$: int [1:3] 1 0 0 ..@ annotation : chr(0) ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. ..@ .Data:List of 4 .. .. .. ..$ : int [1:3] 2 8 1 .. .. .. ..$: int [1:3] 2 2 1 .. .. .. ..$ : int [1:3] 1 1 0 .. .. .. ..$: int [1:3] 1 0 0 > > dim(X) Features Samples 1121049 2 Jianping --On Thursday, January 22, 2009 6:11 PM +0000 Joern Toedling <toedling at="" ebi.ac.uk=""> wrote: > > > Jianping Jin wrote: >> table(probeAnno["5.index"] %in% featureNames(X)) >> >> FALSE >> 21152 > > well, none of the probes seems to be included in the names of the probes > on your arrays. > How did you create the object "X"? Can you show me the output of > str(probeAnno["5.index"]) > str(probeAnno["5.start"]) > str(probeAnno["5.end"]) > ## and for comparison: > str(probeAnno["1.index"]) > str(probeAnno["1.start"]) > > # And what is > str(featureNames(X)) > featureNames(X)[1:30] > str(X) > dim(X) > > >> >> What are feature names in probeAnno? Actually I used a new output file >> from the script you edited to generate probeAnno with no complain: >> >> probeAnno <- >> posToProbeAnno("C:/from_DriveD/Chip- chip/Bultman/allChromExonerateOut_ne >> w.txt") >> >> Creating probeAnno mapping for chromosome 1 10 11 12 13 14 15 16 17 >> 18 19 2 3 4 5 6 7 8 9 X Y Done. >> allChrs <- chromosomeNames(probeAnno) >> genome(probeAnno) <- "M. musculus (mm9)" >> arrayName(probeAnno) <- "2007-02-27_MM8_CpG_Island_Pro_Tiling" > > This looks alright to me. I think the function is working, but somehow > the probeAnno does not seem to match your data ExpressionSet. > > Maybe can you also provide me with the first few lines of this file, > just to be sure? > C:/from_DriveD/Chip-chip/Bultman/allChromExonerateOut_new.txt > > Joern ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104, Campus Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at unc.edu ADD REPLYlink written 10.9 years ago by Jianping Jin60 Hello, this seems to be the source of the problem. The identifiers of the probes that you remapped are of this form 5313_0084_0040 while in the ExpressionSet they are of the form CHR10FS100018407 Were both these types of identifiers given in your array description file (ndf)? If so, and if there's a one-to-one mapping between these, you can probably use these as well as featureNames in the ExpressionSet. You will have to look into the raw RGList type data and see if these identifiers of the type 5313_0084_0040 are also in there. Have a look at tail(RG$genes) If so you can set these identifiers to also be the featureNames of the ExpressionSet by changing the argument "idColumn" of the function preprocess to this column header. Otherwise, if the identifiers of this type 5313_0084_0040 are not unique, you might at the moment lose information from your data, as only uniquely mapped probes are considered for finding enriched regions. In this case, you will probably have to assign the correct unique identifiers to the probe sequences in your Fasta files and you might have to run Exonerate again in this case. Hope this helps. Regards, Joern Jianping Jin wrote: > > >> str(probeAnno["5.index"]) > chr [1:21152] "5313_0084_0040" "5313_0760_0290" "5313_0060_0330" ... >> featureNames(X)[1:30] > [1] "CHR10FS100018407" "CHR10FS100018507" "CHR10FS100018612" > "CHR10FS100018717" > [5] "CHR10FS100018817" "CHR10FS100018927" "CHR10FS100019007" > "CHR10FS100019103" > [9] "CHR10FS100019228" "CHR10FS100019328" "CHR10FS100019428" > "CHR10FS100019503" > [13] "CHR10FS100019603" "CHR10FS100019703" "CHR10FS100019824" > "CHR10FS100019927" > [17] "CHR10FS100020027" "CHR10FS100020117" "CHR10FS010119532" > "CHR10FS010119652" > [21] "CHR10FS010119737" "CHR10FS010119840" "CHR10FS010119947" > "CHR10FS010120052" > [25] "CHR10FS010120142" "CHR10FS010120232" "CHR10FS010120343" > "CHR10FS010120453" > [29] "CHR10FS010120552" "CHR10FS010120652"
Answer: chipAlongChrom problem in Ringo
0
10.9 years ago by
Joern Toedling720 wrote:
Hi Jianping, I presume you created the histogram as we specified in the PLoS CB tutorial article. The error message literally means that the object "y0" does not exist, and you need to create it before drawing the histogram. One option for creating y0, which is the variable holding the threshold for calling ChIP-enriched region, is also given in the tutorial as y0 <- apply(exprs(smoothX), 2, upperBoundNull, prob=0.99) Hope this helps. Joern Jianping Jin wrote: > Thanks Joern. > > I re-ran Exonerate and it worked out for me. > > There is anther question. When I tried to find ChIP-enriched regions > between two experiment conditions with histogram (smoothed reporter > level[log2] versus Percent of Total) by print(h), the error messages > on histograms of both conditions appear: > > Error using packet 1 (or 2) object "y0" not found. > > Both histograms look like normal distribution and very similar, though > condition one shifts a bit left around zero. This may be caused by the > fact that there is no mixture of two underlying distribution was > found. I wanted to make sure if the "no object y(0) being found itself > is the source of the error (so I may want to try other normalization > method) or something else I missed. > > Please take a look at the attached file. Appreciate your help! > > Jianping > -- Joern Toedling EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Phone +44(0)1223 492566 Email toedling at ebi.ac.uk
Hi Joern, You are right. I need to generate y0 for the plot. Here is another trouble: > plot(chersX[[which.max(chersXD$maxLevel)]],smoothX,probeAnno=probeAn no, gff=mm9genes2, paletteName="Dark2", ylim=c(-1,6)) Error in as.double(x) : cannot coerce type 'S4' to vector of type 'double' chipAlongChrom works with expression data while plot works with x and y coordinates. How chersX can be plotted with smoothX? thanks, Jianping --On Tuesday, January 27, 2009 1:47 PM +0000 Joern Toedling <toedling at="" ebi.ac.uk=""> wrote: > Hi Jianping, > > I presume you created the histogram as we specified in the PLoS CB > tutorial article. The error message literally means that the object "y0" > does not exist, and you need to create it before drawing the histogram. > One option for creating y0, which is the variable holding the threshold > for calling ChIP-enriched region, is also given in the tutorial as > y0 <- apply(exprs(smoothX), 2, upperBoundNull, prob=0.99) > Hope this helps. > > Joern > > Jianping Jin wrote: >> Thanks Joern. >> >> I re-ran Exonerate and it worked out for me. >> >> There is anther question. When I tried to find ChIP-enriched regions >> between two experiment conditions with histogram (smoothed reporter >> level[log2] versus Percent of Total) by print(h), the error messages >> on histograms of both conditions appear: >> >> Error using packet 1 (or 2) object "y0" not found. >> >> Both histograms look like normal distribution and very similar, though >> condition one shifts a bit left around zero. This may be caused by the >> fact that there is no mixture of two underlying distribution was >> found. I wanted to make sure if the "no object y(0) being found itself >> is the source of the error (so I may want to try other normalization >> method) or something else I missed. >> >> Please take a look at the attached file. Appreciate your help! >> >> Jianping >> > > -- > Joern Toedling > EMBL - European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge CB10 1SD > United Kingdom > Phone +44(0)1223 492566 > Email toedling at ebi.ac.uk > ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu ADD REPLYlink written 10.9 years ago by Jianping Jin890 Hi Joern, I used the code on the PLos article to summarize the GO terms with the ChIP-enriched regions. But I got some problems in sigGOTable: NFRes <- sigGOTable(NFOnlygenes) . . Level 2: 18 nodes to be scored (17 eliminated genes) Level 1: 1 nodes to be scored (17 eliminated genes) Error in .local(object, ...) : Use: topGOdata, topGOresult_1, topGOresult_2, ..., "parameters". What is the problem and can we fix it? thanks, Jianping --On Tuesday, January 27, 2009 10:52 AM -0500 Jianping Jin <jjin at="" email.unc.edu=""> wrote: > Hi Joern, > > You are right. I need to generate y0 for the plot. > > Here is another trouble: > >> plot(chersX[[which.max(chersXD$maxLevel)]],smoothX,probeAnno=probeA nno, > gff=mm9genes2, paletteName="Dark2", ylim=c(-1,6)) > Error in as.double(x) : > cannot coerce type 'S4' to vector of type 'double' > > chipAlongChrom works with expression data while plot works with x and y > coordinates. How chersX can be plotted with smoothX? > > thanks, > > Jianping > > --On Tuesday, January 27, 2009 1:47 PM +0000 Joern Toedling > <toedling at="" ebi.ac.uk=""> wrote: > >> Hi Jianping, >> >> I presume you created the histogram as we specified in the PLoS CB >> tutorial article. The error message literally means that the object "y0" >> does not exist, and you need to create it before drawing the histogram. >> One option for creating y0, which is the variable holding the threshold >> for calling ChIP-enriched region, is also given in the tutorial as >> y0 <- apply(exprs(smoothX), 2, upperBoundNull, prob=0.99) >> Hope this helps. >> >> Joern >> >> Jianping Jin wrote: >>> Thanks Joern. >>> >>> I re-ran Exonerate and it worked out for me. >>> >>> There is anther question. When I tried to find ChIP-enriched regions >>> between two experiment conditions with histogram (smoothed reporter >>> level[log2] versus Percent of Total) by print(h), the error messages >>> on histograms of both conditions appear: >>> >>> Error using packet 1 (or 2) object "y0" not found. >>> >>> Both histograms look like normal distribution and very similar, though >>> condition one shifts a bit left around zero. This may be caused by the >>> fact that there is no mixture of two underlying distribution was >>> found. I wanted to make sure if the "no object y(0) being found itself >>> is the source of the error (so I may want to try other normalization >>> method) or something else I missed. >>> >>> Please take a look at the attached file. Appreciate your help! >>> >>> Jianping >>> >> >> -- >> Joern Toedling >> EMBL - European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge CB10 1SD >> United Kingdom >> Phone +44(0)1223 492566 >> Email toedling at ebi.ac.uk >> > > > > ################################## > Jianping Jin Ph.D. > Bioinformatics scientist > Center for Bioinformatics > Room 3133 Bioinformatics building > CB# 7104 > University of Chapel Hill > Chapel Hill, NC 27599 > Phone: (919)843-6105 > FAX: (919)843-3103 > E-Mail: jjin at email.unc.edu ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu