Methods for building heatmap for Illumina gene expression data
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affy snp ▴ 640
@affy-snp-2480
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Hi list, I'd appreciate if you could shed some lights on building heatmap for Illumina gene expression data using any bioconductor or R packages. Thanks much, Allen [[alternative HTML version deleted]]
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@sean-davis-490
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On Thu, May 22, 2008 at 2:04 PM, ss <affysnp at="" gmail.com=""> wrote: > Hi list, > > I'd appreciate if you could shed some lights on building heatmap for > Illumina gene expression data using any bioconductor or R packages. Hi, Allen. If you have an ExpressionSet called xset, you can do: heatmap(exprs(xset)[1:25,]) This will give you a heatmap of the first 25 genes. There are numerous references to heatmaps in the bioconductor list archives. I would give a few of those a try. If you run into problems, then you will likely want to post the code that you are using as well as the output of sessionInfo(). Sean
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Hi Sean, I figure heamap() can also be applied if I supply a txt file of Illumina gene expression data based on genes of our interests. I will give it a shot. Thanks a lot. One concern I have about heatmap() is that how it could generate a heatmap with green, black, red colors. Adding some parameters to do so? Regards, Allen On Thu, May 22, 2008 at 4:13 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Thu, May 22, 2008 at 2:04 PM, ss <affysnp@gmail.com> wrote: > > Hi list, > > > > I'd appreciate if you could shed some lights on building heatmap for > > Illumina gene expression data using any bioconductor or R packages. > > Hi, Allen. If you have an ExpressionSet called xset, you can do: > > heatmap(exprs(xset)[1:25,]) > > This will give you a heatmap of the first 25 genes. > > There are numerous references to heatmaps in the bioconductor list > archives. I would give a few of those a try. If you run into > problems, then you will likely want to post the code that you are > using as well as the output of sessionInfo(). > > Sean > [[alternative HTML version deleted]]
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On Thu, May 22, 2008 at 4:21 PM, ss <affysnp at="" gmail.com=""> wrote: > Hi Sean, > > > I figure heamap() can also be applied if I supply a txt file of Illumina > gene > expression data based on genes of our interests. I will give it a shot. > Thanks > a lot. One concern I have about heatmap() is that how it could generate a > heatmap with green, black, red colors. Adding some parameters to do so? Hi, Allen. As for illumina data, I would look into using the beadarray or lumi packages. No reason to use excel for these types of things. As for heatmap, try searching the mailing list here: http://dir.gmane.org/gmane.science.biology.informatics.conductor If you type in the keywords heatmap and color, you will see numerous potential possibilities. Sean
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Hi Sean, Thanks for pointing it out. The reason that I would like to supply with a txt file of Illumina gene expression data is that I find it hard to use either beadarray or lumi to subset gene expression data based on genes of your interest. Please correct me if I am wrong. Anyway, I will check it out. Regards, Allen On Thu, May 22, 2008 at 4:29 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > Hi, Allen. As for illumina data, I would look into using the > beadarray or lumi packages. No reason to use excel for these types of > things. > > As for heatmap, try searching the mailing list here: > > http://dir.gmane.org/gmane.science.biology.informatics.conductor > > If you type in the keywords heatmap and color, you will see numerous > potential possibilities. > > Sean > [[alternative HTML version deleted]]
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On Thu, May 22, 2008 at 7:05 PM, ss <affysnp at="" gmail.com=""> wrote: > Hi Sean, > > Thanks for pointing it out. The reason that I would like to supply with a > txt > file of Illumina gene expression data is that I find it hard to use either > beadarray > or lumi to subset gene expression data based on genes of your interest. > Please > correct me if I am wrong. Anyway, I will check it out. I do not find it particularly difficult to subset genes and samples in either of those packages, and one can always use the exprs() method for each to extract a raw matrix and subset that. For the beadarray package, see the vignette entitled "beadsummary.pdf", paying particular attention to the "BSData" section. Similar methods work with the lumi package. If by "find it hard to use either beadarray or lumi to subset..." you mean that you do not know where to start, I have given a hint above. Also, many of the data classes used in Bioconductor are based on the ExpressionSet class (or the eSet class). There is extensive documentation in the Biobase package for taking subsets of data that will likely apply to both beadarray and lumi subsetting. It is worthwhile working through the examples in the various vignettes and reading help pages if you would like to maximize your productivity with bioconductor. Hope that helps get you going. Sean > On Thu, May 22, 2008 at 4:29 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> >> Hi, Allen. As for illumina data, I would look into using the >> beadarray or lumi packages. No reason to use excel for these types of >> things. >> >> As for heatmap, try searching the mailing list here: >> >> http://dir.gmane.org/gmane.science.biology.informatics.conductor >> >> If you type in the keywords heatmap and color, you will see numerous >> potential possibilities. >> >> Sean > >
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Sean, Thanks for the heads-up. I will read through those documents. Have a great weekend! Allen On Fri, May 23, 2008 at 8:03 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Thu, May 22, 2008 at 7:05 PM, ss <affysnp@gmail.com> wrote: > > Hi Sean, > > > > Thanks for pointing it out. The reason that I would like to supply with a > > txt > > file of Illumina gene expression data is that I find it hard to use > either > > beadarray > > or lumi to subset gene expression data based on genes of your interest. > > Please > > correct me if I am wrong. Anyway, I will check it out. > > I do not find it particularly difficult to subset genes and samples in > either of those packages, and one can always use the exprs() method > for each to extract a raw matrix and subset that. For the beadarray > package, see the vignette entitled "beadsummary.pdf", paying > particular attention to the "BSData" section. Similar methods work > with the lumi package. > > If by "find it hard to use either beadarray or lumi to subset..." you > mean that you do not know where to start, I have given a hint above. > Also, many of the data classes used in Bioconductor are based on the > ExpressionSet class (or the eSet class). There is extensive > documentation in the Biobase package for taking subsets of data that > will likely apply to both beadarray and lumi subsetting. It is > worthwhile working through the examples in the various vignettes and > reading help pages if you would like to maximize your productivity > with bioconductor. > > Hope that helps get you going. > > Sean > > > On Thu, May 22, 2008 at 4:29 PM, Sean Davis <sdavis2@mail.nih.gov> > wrote: > >> > >> Hi, Allen. As for illumina data, I would look into using the > >> beadarray or lumi packages. No reason to use excel for these types of > >> things. > >> > >> As for heatmap, try searching the mailing list here: > >> > >> http://dir.gmane.org/gmane.science.biology.informatics.conductor > >> > >> If you type in the keywords heatmap and color, you will see numerous > >> potential possibilities. > >> > >> Sean > > > > > [[alternative HTML version deleted]]
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