User: perdedorium

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Posts by perdedorium

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Comment: C: GCRMA not working inside tryCatch block in R
... That did the trick! And thanks, I did not know that about tryCatch().  ...
written 11 months ago by perdedorium0
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GCRMA not working inside tryCatch block in R
... I've written a script with a for() loop to process the raw microarray CEL files of five different GEO data sets in R, but it screws up when it gets to the GCRMA processing part. I get a "Was unable to process microarray data" message in my log file, but no error message, despite having an error bloc ...
gcrma simpleaffy trycatch error handling written 11 months ago by perdedorium0 • updated 11 months ago by James W. MacDonald51k
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How to handle big data sets (>10GB) in Bioconductor packages?
... I am running an R script that uses the package MethylMix to download and preprocess all the available methylation data sets from TCGA. However, when I try to process the 450K breast cancer methylation data set (size ~13GB), I get a "Cannot allocate vector of size 12.8 GB" error. I am running R 3.4. ...
big data memory problem methylmix written 12 months ago by perdedorium0 • updated 12 months ago by Martin Morgan ♦♦ 23k
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Can limma/other DE algorithms be used for differential analysis of chemical descriptors?
... If I have two groups of small molecules with different properties, e.g. one can penetrate membranes and the other cannot, and I have an m × n matrix of m small molecules and n descriptors (e.g. polar surface area, molecular weight), can I use, say, limma to identify descriptors that differ between t ...
cheminformatics limma edger deseq2 written 13 months ago by perdedorium0 • updated 13 months ago by Aaron Lun24k
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Bioconductor Cloud AMI - How to Access Microarray Files Stored in Amazon S3 Buckets?
... Hello all, I'm new to Amazon Web Services and cloud computing in general, so please bear with me. My question is, how can I access CEL files stored in an Amazon S3 bucket using the functions in the "oligo" package to create Affybatch objects from CEL files? In other words, in the file path argument ...
bioconductor aws amazon s3 oligo package affybatch written 17 months ago by perdedorium0

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