read subset of affy data
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Xuejun Peng ▴ 20
@xuejun-peng-481
Last seen 9.7 years ago
I have 100 affy arrays and I got an "out-of-memory" error message when I try to batch-read all of them simultaneously. On the other hand, it is really inefficient to read them one by one. Since I have a specific list of genes that I want to read, can I use ReadAffy or some other functions to read the subset of genes directly from .cel files? For a simple example, I only want to read five genes and I know their probe set ID's. Can anyone help? Thanks. Xuejun -- Xuejun Peng, Ph.D. Assistant Staff Biostatistics and epidemiology / Wb4 Cleveland Clinic Foundation 9500 Euclid Avenue Cleveland, OH 44195 Phone: 216-444-9958 Fax: 216-444-8023 E-mail: xpeng@bio.ri.ccf.org, pengx@ccf.org
probe affy probe affy • 1.1k views
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Laurent Gautier ★ 2.3k
@laurent-gautier-29
Last seen 9.7 years ago
On Fri, Oct 17, 2003 at 07:21:10PM -0400, Xuejun Peng wrote: > I have 100 affy arrays and I got an "out-of-memory" error message when I > try to batch-read all of them simultaneously. On the other hand, it is ^^^^^^^^^^^^^^ > really inefficient to read them one by one. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Unless you have customized your own parallel computing/threading routines, the CEL files are read in sequence. > Since I have a specific list of genes that I want to read, can I use > ReadAffy or some other functions to read the subset of genes directly > from .cel files? For a simple example, I only want to read five genes > and I know their probe set ID's. The efficient way is probably to read them one by one (or 10 by 10, or whatever number your memory let you do), and extract and store the probe set of interest each time (function 'probeset'). You can merge the probe sets (see 'class?ProbeSet') Example: l <- list.files(".", "\.cel$") ## list of CEL files all.ppsets <- vector("list", length=length(l)) for (i in seq(along=l)) { abatch <- read.affybatch(filenames=l[i]) all.ppsets[[i]] <- probeset(abatch, c("foo123_at", "foo456_at")) } ## now you just have to merge them... > > Can anyone help? Thanks. I hope this does. L. > > Xuejun > > > -- > Xuejun Peng, Ph.D. > Assistant Staff > Biostatistics and epidemiology / Wb4 > Cleveland Clinic Foundation > 9500 Euclid Avenue > Cleveland, OH 44195 > Phone: 216-444-9958 > Fax: 216-444-8023 > E-mail: xpeng@bio.ri.ccf.org, pengx@ccf.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
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@james-w-macdonald-5106
Last seen 3 days ago
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Look at the code for justRMA in the release version of affy. It is much less memory intensive to iteratively put a cel file in an affybatch, extract the PM data to a matrix and then overwrite the affybatch with the next cel file. You could easily modify the code to only extract the PM data you are interested in into the matrix. Alternatively you could simply use justRMA to get expression values and go from there. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Xuejun Peng <xpeng@bio.ri.ccf.org> 10/17/03 19:22 PM >>> I have 100 affy arrays and I got an "out-of-memory" error message when I try to batch-read all of them simultaneously. On the other hand, it is really inefficient to read them one by one. Since I have a specific list of genes that I want to read, can I use ReadAffy or some other functions to read the subset of genes directly from .cel files? For a simple example, I only want to read five genes and I know their probe set ID's. Can anyone help? Thanks. Xuejun -- Xuejun Peng, Ph.D. Assistant Staff Biostatistics and epidemiology / Wb4 Cleveland Clinic Foundation 9500 Euclid Avenue Cleveland, OH 44195 Phone: 216-444-9958 Fax: 216-444-8023 E-mail: xpeng@bio.ri.ccf.org, pengx@ccf.org _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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you can use read.probematrix directly (its what justRMA calls). it reads either only pm, only mm, or both without creating an AffyBatch. On Sat, 18 Oct 2003, James MacDonald wrote: > Look at the code for justRMA in the release version of affy. It is much > less memory intensive to iteratively put a cel file in an affybatch, > extract the PM data to a matrix and then overwrite the affybatch with > the next cel file. You could easily modify the code to only extract the > PM data you are interested in into the matrix. > > Alternatively you could simply use justRMA to get expression values and > go from there. > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > >>> Xuejun Peng <xpeng@bio.ri.ccf.org> 10/17/03 19:22 PM >>> > I have 100 affy arrays and I got an "out-of-memory" error message when I > > try to batch-read all of them simultaneously. On the other hand, it is > really inefficient to read them one by one. > Since I have a specific list of genes that I want to read, can I use > ReadAffy or some other functions to read the subset of genes directly > from .cel files? For a simple example, I only want to read five genes > and I know their probe set ID's. > > Can anyone help? Thanks. > > Xuejun > > > -- > Xuejun Peng, Ph.D. > Assistant Staff > Biostatistics and epidemiology / Wb4 > Cleveland Clinic Foundation > 9500 Euclid Avenue > Cleveland, OH 44195 > Phone: 216-444-9958 > Fax: 216-444-8023 > E-mail: xpeng@bio.ri.ccf.org, pengx@ccf.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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i forgot to mention, this is in the devel version. On Sat, 18 Oct 2003, Rafael A. Irizarry wrote: > you can use read.probematrix directly (its what justRMA calls). > it reads either only pm, only mm, or both without creating an > AffyBatch. > > > On Sat, 18 Oct 2003, James MacDonald wrote: > > > Look at the code for justRMA in the release version of affy. It is much > > less memory intensive to iteratively put a cel file in an affybatch, > > extract the PM data to a matrix and then overwrite the affybatch with > > the next cel file. You could easily modify the code to only extract the > > PM data you are interested in into the matrix. > > > > Alternatively you could simply use justRMA to get expression values and > > go from there. > > > > HTH, > > > > Jim > > > > > > > > James W. MacDonald > > Affymetrix and cDNA Microarray Core > > University of Michigan Cancer Center > > 1500 E. Medical Center Drive > > 7410 CCGC > > Ann Arbor MI 48109 > > 734-647-5623 > > >>> Xuejun Peng <xpeng@bio.ri.ccf.org> 10/17/03 19:22 PM >>> > > I have 100 affy arrays and I got an "out-of-memory" error message when I > > > > try to batch-read all of them simultaneously. On the other hand, it is > > really inefficient to read them one by one. > > Since I have a specific list of genes that I want to read, can I use > > ReadAffy or some other functions to read the subset of genes directly > > from .cel files? For a simple example, I only want to read five genes > > and I know their probe set ID's. > > > > Can anyone help? Thanks. > > > > Xuejun > > > > > > -- > > Xuejun Peng, Ph.D. > > Assistant Staff > > Biostatistics and epidemiology / Wb4 > > Cleveland Clinic Foundation > > 9500 Euclid Avenue > > Cleveland, OH 44195 > > Phone: 216-444-9958 > > Fax: 216-444-8023 > > E-mail: xpeng@bio.ri.ccf.org, pengx@ccf.org > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >
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