Hi netters! I would like to know if there r any packages in bioconductor that can perform single-color microarray analysis on the gene level instead of the probe level. That's to say, I've had a matrix with each column representing the expression values for a list of genes in a given condition and each row represents the expression value of a gene across different conditions. I wanna do all the analysis like normalization, plotting....etc. I was at a loss what packages should I use? The affy package generally handles probe-level data - they require the colomns to be signals for PM and MM probes, not the expression level of genes. The limma package provides some tools to analysis my data, such as normalizeQuantiles, etc. But limma generally handles two-color microarray data, so there's not much can be done with my data. For example, limma's plotting functions usually require both Red and Green signal levels. I'm a bit surprised to see that there seems no packages to handle single-color microarray data on the gene level. Could anyone help me? Thanks a lot!

On Mar 3, 2005, at 1:27 AM, zhihua li wrote: > Hi netters! > > I would like to know if there r any packages in bioconductor that can > perform single-color > microarray analysis on the gene level instead of the probe level. > That's to say, I've had a matrix with each column representing the > expression values for a list of genes in a given condition and each > row represents the expression value of a gene across different > conditions. I wanna do all the analysis like normalization, > plotting....etc. I was at a loss what packages should I use? The affy > package generally handles probe-level data - they require the colomns > to be signals for PM and MM probes, not the expression level of genes. > The limma package provides some tools to analysis my data, such as > normalizeQuantiles, etc. But limma generally handles two-color > microarray data, so there's not much can be done with my data. For > example, limma's plotting functions usually require both Red and Green > signal levels. I'm a bit surprised to see that there seems no packages > to handle single-color microarray data on the gene level. Could anyone > help me? Thanks a lot! Actually, limma will do single-channel analyses just fine. If you have a matrix of expression values (genes in rows, samples in columns) appropriately normalized, you can happily use limma with that matrix. After all, the affy package ultimately produces just such a matrix. While the affy package does provide many bells and whistles specific to affy, there are many tools that you can use to evaluate your date. Look at limma's plotDensities function, which I think will let you plot single-channel data. You can also use R's built-in plotting to do all-vs-all scatterplots to look at distribution issues. You can threshold based on expression just using simple R subsetting. And the full power of limma's linear models are not really platform-dependent, as I mentioned; they require only a matrix of numbers. So, I the tools are there. Read the single-channel sections of the limma manual, but where an eset (or expression set, in affy parlance) is used, you can simply use your numeric matrix of expression values. Hope this helps. Sean

This is simply not true. I almost always work with a matrix of normalised expressions (row representing probesets and columns representing the arrays). And I mostly work with Affymetrix data. I have recently started using LIMMA and found it to be intuitive and easy. I would consider "normalization" to be part of the pre-processing stage and not the analysis. I am afraid that once you have done the summary step (16 probe pairs into a single probeset), you cannot re-normalise without the CEL files. It is true that the LIMMA documentations focuses more on two-colour arrays because they are more difficult to analyse because of the more complex designs that are possible due to dye assignment issue. Having said that, the LIMMA documentations are pretty clear (with many example) how to analyse the Affymetrix data. See Section 9 onwards of the LIMMA User Guide. There is a very simple example in Section 9.2. Regards, Adai On Thu, 2005-03-03 at 06:27 +0000, zhihua li wrote: > Hi netters! > > I would like to know if there r any packages in bioconductor that can > perform single-color > microarray analysis on the gene level instead of the probe level. That's to > say, I've had a matrix with each column representing the expression values > for a list of genes in a given condition and each row represents the > expression value of a gene across different conditions. I wanna do all the > analysis like normalization, plotting....etc. I was at a loss what packages > should I use? The affy package generally handles probe-level data - they > require the colomns to be signals for PM and MM probes, not the expression > level of genes. The limma package provides some tools to analysis my data, > such as normalizeQuantiles, etc. But limma generally handles two- color > microarray data, so there's not much can be done with my data. For example, > limma's plotting functions usually require both Red and Green signal > levels. I'm a bit surprised to see that there seems no packages to handle > single-color microarray data on the gene level. Could anyone help me? > Thanks a lot! > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

>Date: Thu, 03 Mar 2005 06:27:13 +0000 >From: "zhihua li" <lzhtom@hotmail.com> >Subject: [BioC] single color microarray analysis >To: bioconductor@stat.math.ethz.ch > >Hi netters! > >I would like to know if there r any packages in bioconductor that can >perform single-color >microarray analysis on the gene level instead of the probe level. That's to >say, I've had a matrix with each column representing the expression values >for a list of genes in a given condition and each row represents the >expression value of a gene across different conditions. I wanna do all the >analysis like normalization, plotting....etc. I was at a loss what packages >should I use? The affy package generally handles probe-level data - they >require the colomns to be signals for PM and MM probes, not the expression >level of genes. The limma package provides some tools to analysis my data, >such as normalizeQuantiles, etc. But limma generally handles two- color >microarray data, so there's not much can be done with my data. For example, >limma's plotting functions usually require both Red and Green signal >levels. Mmm. Almost all limma package functions will operate on plain matrices, when this is at all sensible. This means you can store your data in a matrix for which rows are genes and columns are arrays. Then you have access to normalization (normalizeBetweenArrays), differential expression (lmFit etc) and plotting (plotMA). And some functions from the affy package such as plotDensity() will work for you as well. What was it that you wanted to do that you couldn't? Gordon > I'm a bit surprised to see that there seems no packages to handle >single-color microarray data on the gene level. Could anyone help me? >Thanks a lot!

>Date: Thu, 03 Mar 2005 06:27:13 +0000 >From: "zhihua li" <lzhtom@hotmail.com> >Subject: [BioC] single color microarray analysis >To: bioconductor@stat.math.ethz.ch > >Hi netters! > >I would like to know if there r any packages in bioconductor that can >perform single-color >microarray analysis on the gene level instead of the probe level. That's to >say, I've had a matrix with each column representing the expression values >for a list of genes in a given condition and each row represents the >expression value of a gene across different conditions. I wanna do all the >analysis like normalization, plotting....etc. I was at a loss what packages >should I use? The affy package generally handles probe-level data - they >require the colomns to be signals for PM and MM probes, not the expression >level of genes. The limma package provides some tools to analysis my data, >such as normalizeQuantiles, etc. But limma generally handles two- color >microarray data, so there's not much can be done with my data. For example, >limma's plotting functions usually require both Red and Green signal >levels. I'm a bit surprised to see that there seems no packages to handle >single-color microarray data on the gene level. Just a few more comments. As I've already written, I think the functionality for single-channel microarray data is there, you just haven't dug deep enough. What I think you're expressing surprise at is the fact that the functionality is implicit rather than explicit, i.e., it isn't advertised. I think the reason for this is that there has, so far, been no individual single-channel platform which has become sufficiently widely used to provoke dedicated functions or capabilities in Bioconductor packages. For example, there are no read functions designed for single-channel data because we don't know which platform to cater for. Perhaps the Codelink platform will change this. Gordon > Could anyone help me? >Thanks a lot!

>>Date: Thu, 03 Mar 2005 06:27:13 +0000 >>From: "zhihua li" <lzhtom@hotmail.com> >>Subject: [BioC] single color microarray analysis >>To: bioconductor@stat.math.ethz.ch >> >>Hi netters! >> >>I would like to know if there r any packages in bioconductor that can >>perform single-color >>microarray analysis on the gene level instead of the probe level. That's to >>say, I've had a matrix with each column representing the expression values >>for a list of genes in a given condition and each row represents the >>expression value of a gene across different conditions. I wanna do all the >>analysis like normalization, plotting....etc. I was at a loss what packages >>should I use? The affy package generally handles probe-level data - they >>require the colomns to be signals for PM and MM probes, not the expression >>level of genes. The limma package provides some tools to analysis my data, >>such as normalizeQuantiles, etc. But limma generally handles two- color >>microarray data, so there's not much can be done with my data. For example, >>limma's plotting functions usually require both Red and Green signal >>levels. I'm a bit surprised to see that there seems no packages to handle >>single-color microarray data on the gene level. > >Just a few more comments. As I've already written, I think the >functionality for single-channel microarray data is there, you just >haven't dug deep enough. What I think you're expressing surprise at is the >fact that the functionality is implicit rather than explicit, i.e., it >isn't advertised. I think the reason for this is that there has, so far, >been no individual single-channel platform which has become sufficiently >widely used to provoke dedicated functions or capabilities in Bioconductor >packages. I meant, no single-channel platform other than Affymetrix, of course ... Gordon > For example, there are no read functions designed for single- channel > data because we don't know which platform to cater for. Perhaps the > Codelink platform will change this. > >Gordon > >> Could anyone help me? >>Thanks a lot!