use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis
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Dan Strumpf ▴ 70
@dan-strumpf-3246
Last seen 7.4 years ago
Hello, I am new to exon array analysis and have used the huex10stv2cdf_1.15.0.tar.gz package (downloaded from http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz )as a cdf source/mapping for processing Human exon array data within 'affy' package. Processing went smoothly without any error messages. Noticed some communication about this package in Oct. 2007, and am not clear if results using it are relaible. I am interested in processing Human exon array data also with gcRMA and am wondering if should use the above package or use xps/exonmap/oligo instead? Would like to know also what are to options for differential expression analysis equivalent to samr limma or RankProd for paired samples from within exon array analysis packages or could the preprocessed/normalized data be exported and used with xps/exonmap/oligo packages. Thanks, Dan
cdf limma RankProd cdf limma RankProd • 829 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
Hi Dan, Dan Strumpf wrote: > Hello, > > I am new to exon array analysis and have used the huex10stv2cdf_1.15.0.tar.gz > package (downloaded from > http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz > )as a cdf source/mapping for processing Human exon array data within 'affy' > package. Processing went smoothly without any error messages. Noticed some > communication about this package in Oct. 2007, and am not clear if results > using it are relaible. I don't know anything about that cdf, but if it is similar to the modified cdf that you can get from PICR for exonmap, you should get pretty much the same values, as exonmap uses the affy package and a modified cdf to compute expression values. The upside to using exonmap is that you have ways to map the probesets to their location on the genome, and could thereby filter out those that hit what are considered to be inter-genic or intronic positions. I don't know if you will be able to use gcrma, as there are no MM probes on the exon chips. Instead they just have two sets of probes that are designed to measure background. > I am interested in processing Human exon array data also with gcRMA and am > wondering if should use the above package or use xps/exonmap/oligo instead? > Would like to know also what are to options for differential expression > analysis equivalent to samr limma or RankProd for paired samples from within > exon array analysis packages or could the preprocessed/normalized data be > exported and used with xps/exonmap/oligo packages. Pre-processing and differential expression are in general handled by different packages. For instance, you don't use the affy or gcrma package to look for differentially expressed genes, and the same holds true for xps, exonmap, and oligo. That said, there isn't really that much different between the exon chip data and the 3' biased arrays, so tools like limma and RankProd should be fine for analyzing these data. Best, Jim > > Thanks, > > Dan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662
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Hi Jim, Thanks for your reply and insight. I will check out your suggestions, and evaluate to best strategy for generating the expression data set and then analysing it 'externally'. Best, Dan James W. MacDonald wrote: > Hi Dan, > > Dan Strumpf wrote: >> Hello, >> >> I am new to exon array analysis and have used the >> huex10stv2cdf_1.15.0.tar.gz package (downloaded from >> http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz >> )as a cdf source/mapping for processing Human exon array data within >> 'affy' package. Processing went smoothly without any error messages. >> Noticed some communication about this package in Oct. 2007, and am not >> clear if results using it are relaible. > > I don't know anything about that cdf, but if it is similar to the > modified cdf that you can get from PICR for exonmap, you should get > pretty much the same values, as exonmap uses the affy package and a > modified cdf to compute expression values. > > The upside to using exonmap is that you have ways to map the probesets > to their location on the genome, and could thereby filter out those that > hit what are considered to be inter-genic or intronic positions. > > I don't know if you will be able to use gcrma, as there are no MM probes > on the exon chips. Instead they just have two sets of probes that are > designed to measure background. > > >> I am interested in processing Human exon array data also with gcRMA >> and am wondering if should use the above package or use >> xps/exonmap/oligo instead? Would like to know also what are to options >> for differential expression analysis equivalent to samr limma or >> RankProd for paired samples from within exon array analysis packages >> or could the preprocessed/normalized data be exported and used with >> xps/exonmap/oligo packages. > > Pre-processing and differential expression are in general handled by > different packages. For instance, you don't use the affy or gcrma > package to look for differentially expressed genes, and the same holds > true for xps, exonmap, and oligo. > > That said, there isn't really that much different between the exon chip > data and the 3' biased arrays, so tools like limma and RankProd should > be fine for analyzing these data. > > Best, > > Jim > > >> >> Thanks, >> >> Dan >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >
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