You can get these from Affy at: http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu 133 There are downloadable FASTA sequence files for hgu133a. These need to be prepared using the formatdb command that comes with the blast package from NCBI. Depending on how you want to think of your problem, it may make more sense to blast these sequences against your sequences of interest (a more typical analysis, I think). Sean On 7/5/04 10:39 AM, "S Peri" <biocperi@yahoo.com> wrote: > Hi Group, > I want to create a database of Affy probe sequences > that can be used to BLAST (NCBI local BLAST) my > sequence files against this database. For this, I > downloaded the XML based hgu133a (1.5.0)Human > gzipped XML data from BioConductor. The file > extension is weird which is hgu133plus2.xml.gz.xml, > this is not in gzipped format. When I try to open I > can see XML tags and I do not see any sequence data. > This looks like annotation data. > > > Could any one please suggest which is the correct file > that has the sequence data for all affy chips. Also, > is there some way to format that sequence data for > NCBI BLASTable database. > > Thank you. > > Cheers > SP > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Dear SP, The problem is that the set commands work on vectors, and you have dataframes. Try CiS=intersect(as.vector(c),as.vector(s)) Also, avoid using "c" as a variable name, as it is also the name of an important function, concatenate, that allows you to create vectors and also change objects from matrices to vectors. --Naomi Altman At 08:21 PM 7/7/2004 -0700, S Peri wrote: >Hello group, > I am learning R and I am new to many concepts.I face >the following errors when I am trying to execute the >following. I have 4 text files with protein accession >numbers. I wanted to represent them in a venn diagram >and for that I using intersect and setdiff functions. > >My data looks like this: > >file1.txt (c): >NP_000005 >NP_000020 >NP_000030 >NP_000053 > >file2.txt(e): >NP_000005 >NP_000020 >NP_000030 >NP_000031 >NP_000053 >NP_000055 >NP_000087 > >file3.txt(h): >NP_000005 >NP_000020 >NP_000030 >NP_000053 >NP_000055 >NP_000057 >NP_000087 > >file4.txt (s): >NP_000005 >NP_000020 >NP_000030 >NP_000033 >NP_000053 >NP_000055 >NP_000087 >NP_000168 > > >Now I did the following FIRST time: >c=read.table("file1.txt") >e=read.table("file2.txt") >s=read.table("file4.txt") >h=read.table("file3.txt") > > > class(c) >[1] "data.frame" > > class(s) >[1] "data.frame" > > CiS=intersect(c,s) > > CiS >NULL data frame with 0 rows >##### Why am I getting NULL data error. I know there >are common elements between c and S. ########## > > > CiS<-intersect(read.matrix(c,s)) >Error in unique(y[match(x, y, 0)]) : Argument "y" is >missing, with no default > > CiS<-intersect(read.frame(c,s)) >Error in unique(y[match(x, y, 0)]) : Argument "y" is >missing, with no default > >##### Why am I getting this error. > > > >Second thing I did: > >I loaded the data as data.frame instead read.table(). >Again I never get intersection of C,E and S,H. > > >Can any one please help me. >thank you > >SP > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111