Question: Anyone have a GO slim list for Affy HG-U133A or HG-U133Av2?
0
gravatar for Ken Termiso
14.7 years ago by
Ken Termiso250
Ken Termiso250 wrote:
Hi Sean, Maybe from now on I'll just email you directly instead of the mailing list :) Thanks for your reply...I did something similar to get what I wanted and I think it's pretty simple (provided you're using the affy annotation file): Say I wanted to get a list of all genes related to cell death: # "ann" is a data frame containing the affy annotation file HG-U133A_2_annot_csv.zip off their website i <- grep("death", as.vector(ann$Gene.Ontology.Biological.Process)) j <- grep("apoptosis", as.vector(ann$Gene.Ontology.Biological.Process)) k <- union(i,j) k <- sort(k) #optional, but the union arg returns unsorted te <- data.frame() te <- ann[k,] Now "te" is a data frame that contains the genes that have either "death" or "apoptosis" mentioned in GO Biol. Proc. I see there in your reply that you are using the annotate library -- the only annotation I've used is the affy file, which contains a lot of fields -- do you recommend using the annotate library over this? I've been using the affy file b/c it's a simple .csv file and thus is pretty straightforward to work with in R. Thanks again, Ken >From: Sean Davis <sdavis2@mail.nih.gov> >To: "Ken Termiso" <jerk_alert@hotmail.com> >CC: bioconductor@stat.math.ethz.ch >Subject: Re: [BioC] Anyone have a GO slim list for Affy HG-U133A or >HG-U133Av2? Date: Thu, 24 Feb 2005 12:47:57 -0500 > >Ken, > >You could certainly produce such a list by repeating what they have done on >that website. For example, for GO_slim, biologic process 3 (cell cycle and >proliferation): > >library(hgu133a) >library(annotate) >genes <- >unlist(lookUp(c('GO:0007049','GO:0008283'),'hgu133a','GO2ALLPROBES')) >genes <- genes[!duplicated(genes)] > >This will contain the genes in cell cycle and proliferation. It wouldn't >be hard to automate this process for each category. For those categories >that include EXCLUDE descriptions, you can use R set commands like %in% to >get the sets you want. > >Sean > >On Feb 24, 2005, at 11:44 AM, Ken Termiso wrote: > >>Hi, >> >>I'm using the affy HG-U133A_2_annot_csv.zip annotation file to annotate my >>data (which may be a bad idea to begin with..?), and would like to be able >>to use the GO slim categories to annotate my data (see >>http://www.spatial.maine.edu/~mdolan/MGI_GO_Slim.html), instead of the >>extremely detailed GO categories already present in the affymetrix file - >>Gene.Ontology.Biological.Process, Gene.Ontology.Cellular.Component, >>Gene.Ontology.Molecular.Function. >> >>Basically, the issue is that I don't want to have the 2,000 - 5,000 >>different annotation groups in my file. I want to be able to run subset() >>on very general groups, like "development" or "death". >> >>Thanks in advance, >>Ken >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink modified 14.7 years ago by Aedin Culhane310 • written 14.7 years ago by Ken Termiso250
Answer: Anyone have a GO slim list for Affy HG-U133A or HG-U133Av2?
0
gravatar for Aedin Culhane
14.7 years ago by
Aedin Culhane310
Aedin Culhane310 wrote:
Dear Ken I was recently doing the same kind of this. I needed to get counts of genes in go slim classes on an old Affy hu6800 chip and compare this to the distribution of genes in the genome. To get GO slim counts I did the following library(annaffy) library(hu6800) # I got a listing of the GO Slim classes from the Integr8 website at EBI. # http://www.ebi.ac.uk/integr8/GOAnalysisPage.do?orgProteomeID=25 and saved this and a comma # separated file genome.go<-read.csv( "GO_count_ebi_integr8.csv") add.counts<-function(xx.list, ref){ n = length(ref) out=vector() for (i in 1:n) { go= as.character(ref[i]) if(length(xx.list) > 0){ go.count= length(xx.list[go][[1]]) out[i] = go.count } } return(out) } res.go$hu68002allprobe = add.counts(as.list(hu6800GO2ALLPROBES), genome.go[,1]) res.go$hu68002probe = add.counts(as.list(hu6800GO2PROBE), genome.go[,1]) Otherwise, you may wish to browse the equivalent to as.list(hu6800GO2ALLPROBES) as.list(hu6800GO2PROBE) The library(hgu133a_2) will have an equivalent hgu133a_2GO2ALLPROBES etc Hope this helps Aedin
ADD COMMENTlink written 14.7 years ago by Aedin Culhane310
Hi, I have a bunch of .INT files. I wrote a python script to chop the header information and other outlier probe information from a CEL file and I wrote only the intensities from CEL files to .INT files. Now my aim is to collect all the intensities from these 100 INT files and write a matrix. I wrote a small function, that goes to a directory picks up all the .INT files and write a matrix. I could not write this properly. Could any one correct me. Function: > cycle<-function(file.path=".",file.pattern="*.int") + { + files.2.process<-dir(path=file.path,pattern=file.pattern) + forfile.name in files.2.process) + { + current.file<-read.delimfile.name,sep='\t') + { + my_data<-data.frame(current.file) + } + } + } > data<-cycle("C:\Documents and Settings\Marray-affy\Database\U133\Bronchial_Epithelia\int\",".int") Error: syntax error Please help me. thanks S.Peri
ADD REPLYlink written 14.7 years ago by S Peri320
Does read.affybatch not work for you? Sean On Feb 25, 2005, at 1:01 PM, S Peri wrote: > Hi, > > I have a bunch of .INT files. I wrote a python script > to chop the header information and other outlier probe > information from a CEL file and I wrote only the > intensities from CEL files to .INT files. > Now my aim is to collect all the intensities from > these 100 INT files and write a matrix. > > I wrote a small function, that goes to a directory > picks up all the .INT files and write a matrix. I > could not write this properly. Could any one correct > me. > > Function: >> cycle<-function(file.path=".",file.pattern="*.int") > + { > + > files.2.process<-dir(path=file.path,pattern=file.pattern) > + forfile.name in files.2.process) > + { > + current.file<-read.delimfile.name,sep='\t') > + { > + my_data<-data.frame(current.file) > + } > + } > + } >> data<-cycle("C:\Documents and > Settings\Marray-affy\Database\U133\Bronchial_Epithelia\int\",".int") > Error: syntax error > > > Please help me. > > thanks > > S.Peri > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD REPLYlink written 14.7 years ago by Sean Davis21k
what can trigger the following error? I have imported many genepix files without any problem >> RG.new.gpr <- read.maimages(files.new,"genepix",wt.fun=wtflags(0.1)) >Error in "[.data.frame"(obj, , columns$Gf) : > undefined columns selected This is with limma version 1.8.22 Peter P.S. Here is a snippet of the first .gpr file: ATF 1.0 29 56 "Type=GenePix Results 3" "DateTime=2005/01/26 14:13:02" "Settings=" "GalFile=C:\Axon\Params\ImmunArray2.gal" "PixelSize=10" "Wavelengths=635 594" "ImageFiles=Y:\one\two\IMMUNOARRAY\26.01.05\13012006_SEKA0137-01_Cy5_2 6.01.05.tif.tif 0 Y:\one\two\IMMUNOARRAY\26.01.05\13012006_HURR_Cy3_26.01.05.tif 0" "NormalizationMethod=None" "NormalizationFactors=1 1" "JpegImage=C:\Axon\Data\13012006_SEKA0137-01_Cy5_0026.jpg" "StdDev=Type 1" "RatioFormulations=W1/W2 (635/594)" "FeatureType=Circular" "Barcode=" "BackgroundSubtraction=LocalFeature" "ImageOrigin=0, 0" "JpegOrigin=1190, 940" "Creator=GenePix Pro 6.0.0.76" "Scanner=4000 680056" "FocusPosition=0" "Temperature=0" "LinesAveraged=1" "Comment=" "PMTGain=0 0" "ScanPower=100 100" "LaserPower=0 0" "Filters= " "ScanRegion=0,0,2022,3665" "Supplier=" "Block" "Column" "Row" "Name" "ID" "X" "Y" "Dia." "F635 Median" "F635 Mean" "F635 SD" "F635 CV" "B635" "B635 Median" "B635 Mean" "B635 SD" "B635 CV" "% > B635+1SD" "% > B635+2SD" "F635 % Sat." "F594 Median" "F594 Mean" "F594 SD" "F594 CV" "B594" "B594 Median" "B594 Mean" "B594 SD" "B594 CV" "% > B594+1SD" "% > B594+2SD" "F594 % Sat." "Ratio of Medians (635/594)" "Ratio of Means (635/594)" "Median of Ratios (635/594)" "Mean of Ratios (635/594)" "Ratios SD (635/594)" "Rgn Ratio (635/594)" "Rgn R2 (635/594)" "F Pixels" "B Pixels" "Circularity" "Sum of Medians (635/594)" "Sum of Means (635/594)" "Log Ratio (635/594)" "F635 Median - B635" "F594 Median - B594" "F635 Mean - B635" "F594 Mean - B594" "F635 Total Intensity" "F594 Total Intensity" "SNR 635" "SNR 594" "Flags" "Normalize" "Autoflag" 1 1 1 "DUSP2:Hs.1183:AA759046" "1321598" 1540 1160 100 2528 2522 1254 49 0 0 90 154 171 100 97 0 1971 1990 1077 54 0 0 59 123 208 100 97 0 1.283 1.267 1.363 1.339 2.275 1.272 0.575 80 546 100 4499 4512 0.359 2528 1971 2522 1990 201729 159237 15.792 15.699 0 0 0 1 2 1 "DUSP2:Hs.1183:AA759046" "1321598" 1750 1170 120 2686 2625 1525 58 0 0 84 174 207 97 95 0 1841 2014 1266 62 0 0 47 106 225 96 95 0 1.459 1.303 1.352 1.417 2.660 1.326 0.630 120 693 100 4527 4639 0.545 2686 1841 2625 2014 314976 241629 14.603 18.557 0 0 0 1 3 1 "MYL4:Hs.356717:AA705225" "461425" 1940 1160 110 7604 7657 2219 28 0 0 77 142 184 100 100 0 4055 4284 1390 32 0 0 65 133 204 100 100 0 1.875 1.787 1.684 1.811 1.524 2.029 0.741 80 572 100 11659 11941 0.907 7604 4055 7657 4284 612532 342716 53.380 31.722 0 0 0 1 4 1 "MYL4:Hs.356717:AA705225" "461425" 2140 1160 110 6585 7117 2955 41 0 0 84 167 198 100 100 0 3261 3319 1518 45 0 0 73 164 224 96 95 0 2.019 2.144 2.060 2.423 2.458 2.355 0.736 80 620 100 9846 10436 1.014 6585 3261 7117 3319 569339 265548 42.114 19.793 0 0 0 1 5 1 "PSMB8:Hs.180062:AA181300" "624360" 2350 1160 110 2433 2535 1160 45 0 0 79 146 184 100 98 0 2484 2641 1292 48 0 0 83 219 263 97 97 0 0.979 0.960 0.951 0.989 2.062 0.908 0.637 80 579 100 4917 5176 -0.030 2433 2484 2535 2641 202824 211288 16.822 11.680 0 0 0 1 6 1 "PSMB8:Hs.180062:AA181300" "624360" 2540 1170 120 2155 2327 1336 57 0 0 72 139 193 97 95 0 2260 2256 1207 53 0 0 53 129 243 95 92 0 0.954 1.031 0.961 0.998 2.537 1.101 0.660 120 692 100 4415 4583 -0.069 2155 2260 2327 2256 279193 270688 16.223 17.078 0 0 0 1 7 1 "RAD51C:Hs.412587:R37145" "26997" 2750 1160 90 1743 1788 796 44 0 0 76 143 188 100 98 0 2250 2460 1181 48 0 0 66 161 243 100 98 0 0.775 0.727 0.719 0.730 2.097 0.617 0.472 52 420 100 3993 4248 -0.368 1743 2250 1788 2460 92995 127944 11.972 14.870 0 0 0 1 8 1 "RAD51C:Hs.412587:R37145" "26997" 2950 1160 100 1184 1237 725 58 0 0 74 134 181 100 95 0 1938 1806 998 55 0 0 66 147 222 95 92 0 0.611 0.685 0.579 0.692 2.521 0.599 0.484 80 540 100 3122 3043 -0.711 1184 1938 1237 1806 98992 144478 8.679 11.837 0 0 0 1 9 1 "SHC1:Hs.433795:R52961" "40303" 3140 1160 90 2265 2434 1153 47 0 0 83 160 192 100 100 0 2064 2021 1040 51 0 0 73 140 191 98 96 0 1.097 1.204 1.232 1.289 2.207 1.187 0.553 52 414 100 4329 4455 0.134 2265 2064 2434 2021 126582 105071 14.694 13.914 0 0 0 1 10 1 "SHC1:Hs.433795:R52961" "40303" 3350 1170 100 2040 2032 1088 53 0 0 75 122 162 100 100 0 1771 1847 1021 55 0 0 61 119 195 98 96 0 1.152 1.100 1.104 1.141 2.092 1.121 0.569 80 532 100 3811 3879 0.204 2040 1771 2032 1847 162549 147753 16.041 15.008 0 0 0 1 11 1 "TYROBP:Hs.9963:H12338" "148469" 3550 1170 110 15761 14143 5861 41 21 21 106 172 162 100 100 0 744 884 592 66 0 0 42 101 240 91 86 0 21.156 15.975 17.541 19.010 2.619 18.419 0.594 80 590 100 16484 15006 4.403 15740 744 14122 884 1131446 70752 81.610 8.337 0 0 0 1 12 1 "TYROBP:Hs.9963:H12338" "148469" 3750 1170 110 15557 14415 6677 46 0 0 103 178 172 100 100 0 865 916 602 65 0 0 47 131 278 90 80 0 17.985 15.737 16.305 18.014 2.349 18.037 0.619 80 590 100 16422 15331 4.169 15557 865 14415 916 1153181 73243 80.404 6.634 0 0 0
ADD REPLYlink written 14.7 years ago by Pita120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 296 users visited in the last hour