cDNA data

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E Motakis, Mathematics ▴ 190

@e-motakis-mathematics-558

Last seen 10.2 years ago

Dear all, I am currenty working on cDNA microarrays and I would like to check some of the gene differential expression methods (t-tests, SAM etc). Since I do not have any real data, I wonder if there is any webpage that contains free datasets from cDNAs. Thank you in advance, Makis ---------------------- E Motakis, Mathematics E.Motakis@bristol.ac.uk

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ADD COMMENT • link updated 19.5 years ago by Wolfgang Huber ★ 13k • written 19.5 years ago by E Motakis, Mathematics ▴ 190

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Sean Davis 21k

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On May 25, 2005, at 2:08 PM, E Motakis, Mathematics wrote: > Dear all, > > I am currenty working on cDNA microarrays and I would like to check > some of the gene differential expression methods (t-tests, SAM etc). > Since I do not have any real data, I wonder if there is any webpage > that contains free datasets from cDNAs. http://www.ncbi.nih.gov/geo They have a few tens-of-thousands of arrays there, not all cDNA. http://genome-www5.stanford.edu/ Another few thousand arrays.... Sean

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Wolfgang Huber ★ 13k

@wolfgang-huber-3550

Last seen 12 weeks ago

EMBL European Molecular Biology Laborat…

Motakis, Mathematics wrote: > I am currenty working on cDNA microarrays and I would like to check some > of the gene differential expression methods (t-tests, SAM etc). Since I > do not have any real data, I wonder if there is any webpage that > contains free datasets from cDNAs. Dear Makis, You can also check out this one: http://www.ebi.ac.uk/arrayexpress/ and http://www.bioconductor.org/packages/data/experiment/stable/src/contri b/html/ -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber

ADD COMMENT • link 19.5 years ago Wolfgang Huber ★ 13k

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Dear all, Thanks to everyone that responded to my previous email about cDNA microarray databases. Perhaps it is my fault that I was not specific in my query. I would like to find raw cDNA data (not normalized values, not background subtracted, just raw data with their replicates). In the webpages you gave me I found data in the form of log ratios (normalized and background corrected). I wonder if I could find raw cDNA data somewhere. Thank you in advance, Makis ---------------------- E Motakis, Mathematics E.Motakis@bristol.ac.uk

ADD REPLY • link 19.5 years ago E Motakis, Mathematics ▴ 190

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Hi, Makis - You can find raw data (actually combined array layout, raw measurements, and normalized values) on the SMD web and ftp sites. Several BioConductor packages, incuding limma and marray, have functions for reading these tab-delimited text files, or you can easily manipulate them in a spreadsheet application. Go to http://smd.stanford.edu/ and click on "Publications" or "Public Login" to use the various search tools. You'll want the "raw data" files, although the other retrieval options may be useful to you as well. Extensive help documentation is available on the website. Cordially, -- Jeremy Gollub, Ph.D. jgollub@genome.stanford.edu (W) 650/736-0075 On Thu, 26 May 2005, E Motakis, Mathematics wrote: > Dear all, > > Thanks to everyone that responded to my previous email about cDNA > microarray databases. Perhaps it is my fault that I was not specific in my > query. I would like to find raw cDNA data (not normalized values, not > background subtracted, just raw data with their replicates). > > In the webpages you gave me I found data in the form of log ratios > (normalized and background corrected). I wonder if I could find raw cDNA > data somewhere. > > Thank you in advance, > Makis > > > ---------------------- > E Motakis, Mathematics > E.Motakis@bristol.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

ADD REPLY • link 19.5 years ago Jeremy Gollub ▴ 80

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