magetab2bioc error
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@pratibha-mani-4558
Last seen 6.6 years ago
Dear All, I have my files downloaded from Arrayexpress say (E-GEOD-6728). Because it is large in size, I donot want to download it everytime I want to work with the data. My main problem is that I cannot use the load() function as it uses the Bioconductor object generated while downloading from http directly. I want to edit one of the columns in the SDRF file which will make it easier for me to identify case and control samples. I cannot edit the object as it is in binary format. Can anyone please help as whenver I use magetab2bioc() it gives me an error while using my local files stored? Thanks in advance. [[alternative HTML version deleted]]
ArrayExpress ArrayExpress • 458 views
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@wolfgang-huber-3550
Last seen 9 days ago
EMBL European Molecular Biology Laborat…
Dear Pratibha Mani thank you for the feedback. I think you will increase your chance of getting help if you ask a more specific question. Please provide a reproducible example (R code) that produces your problem, and an exact description (error message?) of what you think the problem is. Also, sessionInfo(). You mention that you want to manipulate some column(s) in the array metadata. Are you sure you are familiar enough with R and with the ExpressionSet class defined in the Biobase package to conclude that you cannot easily do this in R? Best wishes Wolfgang pratibha mani scripsit 24/03/11 07:42: > Dear All, > > I have my files downloaded from Arrayexpress say (E-GEOD-6728). Because it > is large in size, I donot want to download it everytime I want to work with > the data. My main problem is that I cannot use the load() function as it > uses the Bioconductor object generated while downloading from http directly. > > I want to edit one of the columns in the SDRF file which will make it easier > for me to identify case and control samples. I cannot edit the object as it > is in binary format. Can anyone please help as whenver I use magetab2bioc() > it gives me an error while using my local files stored? > > Thanks in advance. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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