Dear Colleagues, I would like to select genes based on the Affymetrix calls (mas5call-function in affy package). For example, how can I obtain the list of genes/probeIds that have in at least 1 of 20 experiments a present call? Best regards, Katleen De Preter -- No virus found in this outgoing message. Checked by AVG Anti-Virus.

Hello Bioc. I have encountered a problem when I try to use the impute.knn function in the package impute. I have tried to use a matrix with 30000 rows and 2 columns(MS). When I try the command: impute.knn(MS) Then R will crash within a second or so. Does anyone use the imputations in the package impute with any success, or do no one make any imputations at all? Regards Marcus Marcus Gry Bj?rklund Royal Institute of Technology AlbaNova University Center Department of Molecular Biotechnology 106 91 Stockholm, Sweden Phone (office): +46 8 553 783 44 Fax: + 46 8 553 784 81 Visiting address: Roslagstullsbacken 21, Floor 3 Delivery address: Roslagsv?gen 30B Web: http://www.biotech.kth.se/molbio/microarray/index.html -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Katleen De Preter Sent: Thursday, January 13, 2005 9:08 To: bioconductor@stat.math.ethz.ch Subject: [BioC] mas5call select genes Dear Colleagues, I would like to select genes based on the Affymetrix calls (mas5call-function in affy package). For example, how can I obtain the list of genes/probeIds that have in at least 1 of 20 experiments a present call? Best regards, Katleen De Preter -- No virus found in this outgoing message. Checked by AVG Anti-Virus. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Katleen, This is the function I use on a matrix of Affymetrix Absent/Present calls (rows are probesets, columns are chips) number.pres <- function(x) { x[x=="P"] <- 1; x[x!=1] <- 0; return(apply(x,1,function(a) { sum(as.integer(a))})) } # Calculate present/absent calls # They are stored in the exprs slot of PAcalls PAcalls <- mas5calls(raw.data) # This returns a vector where each probeset is listed with the total number of present calls np <- number.pres(PAcalls@exprs) # Get those probesets with at least 1 present call my.list <- names(np[np>0]) The simpleaffy library also provides a function (pairwise.filter) to filter Affymetrix data and one of the parametres allows you to specify a minimum number of chips on which a probeset must be called present Hope this helps Claire > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of > Katleen De Preter > Sent: 13 January 2005 08:08 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] mas5call select genes > > Dear Colleagues, > I would like to select genes based on the Affymetrix calls > (mas5call-function in affy package). For example, how can I > obtain the > list of genes/probeIds that have in at least 1 of 20 experiments a > present call? > Best regards, > Katleen De Preter > > > > > -- > No virus found in this outgoing message. > Checked by AVG Anti-Virus. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

On a slight tangent... Is there really any point using the MAS5 calls in any case as though a useful quality control for the whole experiment singly they seem to have a poor sensitivity/specificity? If you use a variance based filter i.e. filtering all data below a given coefficient of variance this should remove non-expressed data (and inherently uninteresting data depending upon the experiment and design) as it should not vary by much more than the baseline. This is what I do but if anyone thinks this is wrong (or right) I'm interested to know?? -----Original Message----- From: Claire Wilson To: Katleen De Preter Cc: bioconductor@stat.math.ethz.ch Sent: 1/13/05 8:49 AM Subject: RE: [BioC] mas5call select genes Hi Katleen, This is the function I use on a matrix of Affymetrix Absent/Present calls (rows are probesets, columns are chips) number.pres <- function(x) { x[x=="P"] <- 1; x[x!=1] <- 0; return(apply(x,1,function(a) { sum(as.integer(a))})) } # Calculate present/absent calls # They are stored in the exprs slot of PAcalls PAcalls <- mas5calls(raw.data) # This returns a vector where each probeset is listed with the total number of present calls np <- number.pres(PAcalls@exprs) # Get those probesets with at least 1 present call my.list <- names(np[np>0]) The simpleaffy library also provides a function (pairwise.filter) to filter Affymetrix data and one of the parametres allows you to specify a minimum number of chips on which a probeset must be called present Hope this helps Claire > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of > Katleen De Preter > Sent: 13 January 2005 08:08 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] mas5call select genes > > Dear Colleagues, > I would like to select genes based on the Affymetrix calls > (mas5call-function in affy package). For example, how can I > obtain the > list of genes/probeIds that have in at least 1 of 20 experiments a > present call? > Best regards, > Katleen De Preter > > > > > -- > No virus found in this outgoing message. > Checked by AVG Anti-Virus. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -------------------------------------------------------- This email is confidential and intended solely for the use\ ...{{dropped}}