I am trying to use the `olgio` package to process some arrays from GEO/ArrayExpress (E-GEOD-53405 and E-GEOD-61364, among others), and I am running into issues with some of the chip layout packages where they are not available.
In some cases, there might be another chip that is similar enough to use its layout information instead ([3]). Is there a list of which packages one can fall back on? If it is known, how can I tell oligo to use this package instead?
The following are examples:
[1] is looking for the platform name pd.huex.1.0.st.v1, but only pd.huex.1.0.st.v2 is available as a BioConductor package (which might be very similar, can I use v2 instead of v1?)
[2] is looking for the platform pd.u133aaofav2, which is almost identical with pd.ht.hg.u133a according to [3]
Is there any way to process those packages, preferentially with `olgio`, but any other BioConductor package as well?
[1] http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-53405/E-GEOD-53405.raw.3.zip/GSM1290926_t0_rep2.CEL
[2] http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-61364/E-GEOD-61364.raw.1.zip/GSM1503012_05202764006888021105960891.A01.CEL
[3] help with SCAN.UPC and u133aaofav2
Thanks for point 2 - I used the oligo package which doesn't find the correct cdf.
Thanks for point 2 - I used the oligo package which doesn't find the correct cdf.
Right. But that's not what I said to do, is it?
> getGEOSuppFiles("GSE61364") ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE61nnn/GSE61364/suppl/ % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 268M 100 268M 0 0 8623k 0 0:00:31 0:00:31 --:--:-- 7383k % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 8401 100 8401 0 0 4703 0 0:00:01 0:00:01 --:--:-- 4703 > setwd("GSE61364/") > untar("GSE61364_RAW.tar") > library(affy) > dat <- ReadAffy(filenames = list.celfiles()[1:5]) > dat trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/u133aaofav2cdf_2.16.0.tar.gz' Content type 'application/x-gzip' length 1806754 bytes (1.7 MB) ================================================== downloaded 1.7 MB * installing *source* package u133aaofav2cdf ... ** R ** data ** preparing package for lazy loading Creating a generic function for nchar from package base in package S4Vectors ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Creating a generic function for nchar from package base in package S4Vectors * DONE (u133aaofav2cdf) The downloaded source packages are in /data/tmp/RtmpZ2fr9J/downloaded_packages Updating HTML index of packages in '.Library' Making 'packages.html' ... done Creating a generic function for nchar from package base in package S4Vectors AffyBatch object size of arrays=744x744 features (18 kb) cdf=U133AAofAv2 (22944 affyids) number of samples=5 number of genes=22944 annotation=u133aaofav2 notes= > eset <- rma(dat) Background correcting Normalizing Calculating Expression