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Question: Interspecies differential expression of orthologs with Edger
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gravatar for assaf www
3.2 years ago by
assaf www140
assaf www140 wrote:
Dear Edger developers and users, I would like to compare transcription levels of orthologous genes belonging to different species, in order to find significant species-dependent changes in transcription levels. I though of using Edger for such analysis. Specifically, I have the read-counts data for several RNA-Seq samples, for 2 different species (e.g., read counts produced by Htseq-count, and Rsem). I would like to ask: 1) because Edger uses CPM values, which are not normalized by gene- length, and because the length of orthologous genes differ, it would lead to a serious length-dependet bias, and I would ask how to normalize for that. 2) if the above length-bias can be eliminated, and the compared genes are true orthologs, are you aware of any other major problems that should be considered in the above case ? Thanks in advance, Assaf [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.2 years ago by Gordon Smyth32k • written 3.2 years ago by assaf www140
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gravatar for Gordon Smyth
3.2 years ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:
Dear Assaf, In principle, one would incorporate gene length into the edgeR offset matrix, and this would eliminate any length-bias. Best wishes Gordon > Date: Mon, 25 Aug 2014 12:50:36 +0300 > From: assaf www <assafwww at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] Interspecies differential expression of orthologs with > Edger > > Dear Edger developers and users, > > I would like to compare transcription levels of orthologous genes belonging > to different species, in order to find significant species-dependent > changes in transcription levels. I though of using Edger for such analysis. > Specifically, I have the read-counts data for several RNA-Seq samples, for > 2 different species (e.g., read counts produced by Htseq-count, and Rsem). > > I would like to ask: > 1) because Edger uses CPM values, which are not normalized by gene- length, > and because the length of orthologous genes differ, it would lead to a > serious length-dependet bias, and I would ask how to normalize for that. > 2) if the above length-bias can be eliminated, and the compared genes are > true orthologs, are you aware of any other major problems that should be > considered in the above case ? > > > Thanks in advance, > Assaf ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 3.2 years ago by Gordon Smyth32k
Dear Gordon thanks, Suppose I start with the following matrices: # 'counts' is the Rsem filtered counts > counts[1:4,] h0 h1 h2 n0 n1 n2 ENSRNOG00000000021 36 17 20 10 25 38 ENSRNOG00000000024 1283 615 731 644 807 991 ENSRNOG00000000028 26 12 11 18 23 28 ENSRNOG00000000029 22 13 12 16 17 15 # 'geneLength' is the species-specific gene lengths, for species 'h' and 'n': > geneLength[1:3,] h0.length h1.length h2.length n0.length n1.length n2.length ENSRNOG00000000021 1200 1200 1200 1303 1303 1303 ENSRNOG00000000024 1050 1050 1050 3080 3080 3080 ENSRNOG00000000028 1047 1047 1047 1121 1121 1121 does the following code look correct, and may allow allows across species analysis ?: (technically it works, I checked) # quantile normalization: (as in here: http://davetang.org/wiki/tiki- index.php?page=Analysing+digital+gene+expression ) x1 = counts*1000/geneLength library(limma) x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") offset = log(counts+0.1)-log(x2+0.1) ... y <- estimateGLMCommonDisp(y,design,offset=offset) y <- estimateGLMTrendedDisp(y,design,offset=offset) y <- estimateGLMTagwiseDisp(y,design,offset=offset) fit <- glmFit(y,design,offset=offset) ... Thanks in advance for any help.., Assaf [[alternative HTML version deleted]]
ADD REPLYlink written 3.2 years ago by assaf www140
That doesn't look helpful to me. I suggested that you incorporate gene lengths into the offsets, not do quantile normalization of cpms. Sorry, I just don't have time to develop a code example for you. I hope someone else will help. The whole topic of interspecies differential expression is a can of worms. Even if you adjust for gene length, there will still be differences in gc content and mappability between the species. Gordon On Wed, 27 Aug 2014, assaf www wrote: > Dear Gordon thanks, > > Suppose I start with the following matrices: > > # 'counts' is the Rsem filtered counts >> counts[1:4,] > h0 h1 h2 n0 n1 n2 > ENSRNOG00000000021 36 17 20 10 25 38 > ENSRNOG00000000024 1283 615 731 644 807 991 > ENSRNOG00000000028 26 12 11 18 23 28 > ENSRNOG00000000029 22 13 12 16 17 15 > > # 'geneLength' is the species-specific gene lengths, for species 'h' and > 'n': >> geneLength[1:3,] > h0.length h1.length h2.length n0.length n1.length > n2.length > ENSRNOG00000000021 1200 1200 1200 1303 1303 > 1303 > ENSRNOG00000000024 1050 1050 1050 3080 3080 > 3080 > ENSRNOG00000000028 1047 1047 1047 1121 1121 > 1121 > > > does the following code look correct, and may allow allows across species > analysis ?: > (technically it works, I checked) > > # quantile normalization: (as in here: > http://davetang.org/wiki/tiki- index.php?page=Analysing+digital+gene+expression > ) > > x1 = counts*1000/geneLength > library(limma) > x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") > offset = log(counts+0.1)-log(x2+0.1) > > ... > > y <- estimateGLMCommonDisp(y,design,offset=offset) > y <- estimateGLMTrendedDisp(y,design,offset=offset) > y <- estimateGLMTagwiseDisp(y,design,offset=offset) > fit <- glmFit(y,design,offset=offset) > > ... > > > Thanks in advance for any help.., > Assaf > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD REPLYlink written 3.2 years ago by Gordon Smyth32k
Probably wrong, but the reason I thought of using quantile normalization is the need to correct both for the species-length, and library size. On Wed, Aug 27, 2014 at 2:40 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > That doesn't look helpful to me. I suggested that you incorporate gene > lengths into the offsets, not do quantile normalization of cpms. > > Sorry, I just don't have time to develop a code example for you. I hope > someone else will help. > > The whole topic of interspecies differential expression is a can of worms. > Even if you adjust for gene length, there will still be differences in gc > content and mappability between the species. > > Gordon > > > On Wed, 27 Aug 2014, assaf www wrote: > > Dear Gordon thanks, >> >> Suppose I start with the following matrices: >> >> # 'counts' is the Rsem filtered counts >> >>> counts[1:4,] >>> >> h0 h1 h2 n0 n1 n2 >> ENSRNOG00000000021 36 17 20 10 25 38 >> ENSRNOG00000000024 1283 615 731 644 807 991 >> ENSRNOG00000000028 26 12 11 18 23 28 >> ENSRNOG00000000029 22 13 12 16 17 15 >> >> # 'geneLength' is the species-specific gene lengths, for species 'h' and >> 'n': >> >>> geneLength[1:3,] >>> >> h0.length h1.length h2.length n0.length n1.length >> n2.length >> ENSRNOG00000000021 1200 1200 1200 1303 1303 >> 1303 >> ENSRNOG00000000024 1050 1050 1050 3080 3080 >> 3080 >> ENSRNOG00000000028 1047 1047 1047 1121 1121 >> 1121 >> >> >> does the following code look correct, and may allow allows across species >> analysis ?: >> (technically it works, I checked) >> >> # quantile normalization: (as in here: >> http://davetang.org/wiki/tiki-index.php?page=Analysing+ >> digital+gene+expression >> ) >> >> x1 = counts*1000/geneLength >> library(limma) >> x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") >> offset = log(counts+0.1)-log(x2+0.1) >> >> ... >> >> y <- estimateGLMCommonDisp(y,design,offset=offset) >> y <- estimateGLMTrendedDisp(y,design,offset=offset) >> y <- estimateGLMTagwiseDisp(y,design,offset=offset) >> fit <- glmFit(y,design,offset=offset) >> >> ... >> >> >> Thanks in advance for any help.., >> Assaf >> >> > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:10}}
ADD REPLYlink written 3.2 years ago by assaf www140
It works something like this: library(edgeR) y <- DGEList(counts=counts) y <- calcNormFactors(y) # Column correct log gene lengths # Columns of gl should add to zero gl <- log(geneLength) gl <- t(t(gl)-colMeans(gl)) # Combine library sizes, norm factors and gene lengths: offset <- expandAsMatrix(getOffset(y)) offset <- offset + gl Then y$offset <- offset y <- estimateGLMCommonDisp(y,design) etc. Note that I have not tried this myself. It should work in principle from a differential expression point of view. On the other hand, there may be side effects regarding dispersion trend estimation -- I do not have time to explore this. Gordon --------------------------------------------- Professor Gordon K Smyth, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3052, Australia. http://www.statsci.org/smyth On Wed, 27 Aug 2014, assaf www wrote: > Probably wrong, but the reason I thought of using quantile normalization is > the need to correct both for the species-length, and library size. > > > On Wed, Aug 27, 2014 at 2:40 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > >> That doesn't look helpful to me. I suggested that you incorporate gene >> lengths into the offsets, not do quantile normalization of cpms. >> >> Sorry, I just don't have time to develop a code example for you. I hope >> someone else will help. >> >> The whole topic of interspecies differential expression is a can of worms. >> Even if you adjust for gene length, there will still be differences in gc >> content and mappability between the species. >> >> Gordon >> >> >> On Wed, 27 Aug 2014, assaf www wrote: >> >> Dear Gordon thanks, >>> >>> Suppose I start with the following matrices: >>> >>> # 'counts' is the Rsem filtered counts >>> >>>> counts[1:4,] >>>> >>> h0 h1 h2 n0 n1 n2 >>> ENSRNOG00000000021 36 17 20 10 25 38 >>> ENSRNOG00000000024 1283 615 731 644 807 991 >>> ENSRNOG00000000028 26 12 11 18 23 28 >>> ENSRNOG00000000029 22 13 12 16 17 15 >>> >>> # 'geneLength' is the species-specific gene lengths, for species 'h' and >>> 'n': >>> >>>> geneLength[1:3,] >>>> >>> h0.length h1.length h2.length n0.length n1.length >>> n2.length >>> ENSRNOG00000000021 1200 1200 1200 1303 1303 >>> 1303 >>> ENSRNOG00000000024 1050 1050 1050 3080 3080 >>> 3080 >>> ENSRNOG00000000028 1047 1047 1047 1121 1121 >>> 1121 >>> >>> >>> does the following code look correct, and may allow allows across species >>> analysis ?: >>> (technically it works, I checked) >>> >>> # quantile normalization: (as in here: >>> http://davetang.org/wiki/tiki-index.php?page=Analysing+ >>> digital+gene+expression >>> ) >>> >>> x1 = counts*1000/geneLength >>> library(limma) >>> x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") >>> offset = log(counts+0.1)-log(x2+0.1) >>> >>> ... >>> >>> y <- estimateGLMCommonDisp(y,design,offset=offset) >>> y <- estimateGLMTrendedDisp(y,design,offset=offset) >>> y <- estimateGLMTagwiseDisp(y,design,offset=offset) >>> fit <- glmFit(y,design,offset=offset) >>> >>> ... >>> >>> >>> Thanks in advance for any help.., >>> Assaf ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD REPLYlink written 3.2 years ago by Gordon Smyth32k
This is very helpful for me, thanks. A slight change that I made in the code you sent, to avoid some R erros, is # to replace: offset = offset + gl # with: offset = sweep(gl,2,offset,"+") In addition to differential expression tests, I wanted also to extract FPKMs values (and/or normalized CPM values), that would take into account all components of the offset (which if I'm not mistaken are: library_size + TMM + gene_size). I assume rpkm()/cpm() should correct only for library_size + TMM. Is there a possibly "decent" solution for that ? all the best, and thanks, Assaf On Wed, Aug 27, 2014 at 4:45 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > It works something like this: > > library(edgeR) > y <- DGEList(counts=counts) > y <- calcNormFactors(y) > > # Column correct log gene lengths > # Columns of gl should add to zero > > gl <- log(geneLength) > gl <- t(t(gl)-colMeans(gl)) > > # Combine library sizes, norm factors and gene lengths: > > offset <- expandAsMatrix(getOffset(y)) > offset <- offset + gl > > Then > > y$offset <- offset > y <- estimateGLMCommonDisp(y,design) > > etc. > > Note that I have not tried this myself. It should work in principle from > a differential expression point of view. > > On the other hand, there may be side effects regarding dispersion trend > estimation -- I do not have time to explore this. > > Gordon > > --------------------------------------------- > Professor Gordon K Smyth, > Bioinformatics Division, > Walter and Eliza Hall Institute of Medical Research, > 1G Royal Parade, Parkville, Vic 3052, Australia. > http://www.statsci.org/smyth > > On Wed, 27 Aug 2014, assaf www wrote: > > Probably wrong, but the reason I thought of using quantile normalization >> is >> the need to correct both for the species-length, and library size. >> >> >> On Wed, Aug 27, 2014 at 2:40 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> >> wrote: >> >> That doesn't look helpful to me. I suggested that you incorporate gene >>> lengths into the offsets, not do quantile normalization of cpms. >>> >>> Sorry, I just don't have time to develop a code example for you. I hope >>> someone else will help. >>> >>> The whole topic of interspecies differential expression is a can of >>> worms. >>> Even if you adjust for gene length, there will still be differences in gc >>> content and mappability between the species. >>> >>> Gordon >>> >>> >>> On Wed, 27 Aug 2014, assaf www wrote: >>> >>> Dear Gordon thanks, >>> >>>> >>>> Suppose I start with the following matrices: >>>> >>>> # 'counts' is the Rsem filtered counts >>>> >>>> counts[1:4,] >>>>> >>>>> h0 h1 h2 n0 n1 n2 >>>> ENSRNOG00000000021 36 17 20 10 25 38 >>>> ENSRNOG00000000024 1283 615 731 644 807 991 >>>> ENSRNOG00000000028 26 12 11 18 23 28 >>>> ENSRNOG00000000029 22 13 12 16 17 15 >>>> >>>> # 'geneLength' is the species-specific gene lengths, for species 'h' and >>>> 'n': >>>> >>>> geneLength[1:3,] >>>>> >>>>> h0.length h1.length h2.length n0.length n1.length >>>> n2.length >>>> ENSRNOG00000000021 1200 1200 1200 1303 1303 >>>> 1303 >>>> ENSRNOG00000000024 1050 1050 1050 3080 3080 >>>> 3080 >>>> ENSRNOG00000000028 1047 1047 1047 1121 1121 >>>> 1121 >>>> >>>> >>>> does the following code look correct, and may allow allows across >>>> species >>>> analysis ?: >>>> (technically it works, I checked) >>>> >>>> # quantile normalization: (as in here: >>>> http://davetang.org/wiki/tiki-index.php?page=Analysing+ >>>> digital+gene+expression >>>> ) >>>> >>>> x1 = counts*1000/geneLength >>>> library(limma) >>>> x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") >>>> offset = log(counts+0.1)-log(x2+0.1) >>>> >>>> ... >>>> >>>> y <- estimateGLMCommonDisp(y,design,offset=offset) >>>> y <- estimateGLMTrendedDisp(y,design,offset=offset) >>>> y <- estimateGLMTagwiseDisp(y,design,offset=offset) >>>> fit <- glmFit(y,design,offset=offset) >>>> >>>> ... >>>> >>>> >>>> Thanks in advance for any help.., >>>> Assaf >>>> >>> > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:10}}
ADD REPLYlink written 3.2 years ago by assaf www140
Sorry I'm not clear: for getting the FPKMs, I guess I only need to: rpkm(y, gene.length=geneLength, normalized.lib.sizes=T, log=F) But gene.length should here be a vector, while in this case its a matrix. Assaf On Wed, Aug 27, 2014 at 6:14 PM, assaf www <assafwww at="" gmail.com=""> wrote: > This is very helpful for me, thanks. > > A slight change that I made in the code you sent, to avoid some R erros, > is > > # to replace: > offset = offset + gl > # with: > offset = sweep(gl,2,offset,"+") > > In addition to differential expression tests, I wanted also to extract > FPKMs values (and/or normalized CPM values), that would take into account > all components of the offset (which if I'm not mistaken are: library_size + > TMM + gene_size). > I assume rpkm()/cpm() should correct only for library_size + TMM. > Is there a possibly "decent" solution for that ? > > all the best, and thanks, > Assaf > > > > On Wed, Aug 27, 2014 at 4:45 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > >> It works something like this: >> >> library(edgeR) >> y <- DGEList(counts=counts) >> y <- calcNormFactors(y) >> >> # Column correct log gene lengths >> # Columns of gl should add to zero >> >> gl <- log(geneLength) >> gl <- t(t(gl)-colMeans(gl)) >> >> # Combine library sizes, norm factors and gene lengths: >> >> offset <- expandAsMatrix(getOffset(y)) >> offset <- offset + gl >> >> Then >> >> y$offset <- offset >> y <- estimateGLMCommonDisp(y,design) >> >> etc. >> >> Note that I have not tried this myself. It should work in principle from >> a differential expression point of view. >> >> On the other hand, there may be side effects regarding dispersion trend >> estimation -- I do not have time to explore this. >> >> Gordon >> >> --------------------------------------------- >> Professor Gordon K Smyth, >> Bioinformatics Division, >> Walter and Eliza Hall Institute of Medical Research, >> 1G Royal Parade, Parkville, Vic 3052, Australia. >> http://www.statsci.org/smyth >> >> On Wed, 27 Aug 2014, assaf www wrote: >> >> Probably wrong, but the reason I thought of using quantile normalization >>> is >>> the need to correct both for the species-length, and library size. >>> >>> >>> On Wed, Aug 27, 2014 at 2:40 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> >>> wrote: >>> >>> That doesn't look helpful to me. I suggested that you incorporate gene >>>> lengths into the offsets, not do quantile normalization of cpms. >>>> >>>> Sorry, I just don't have time to develop a code example for you. I hope >>>> someone else will help. >>>> >>>> The whole topic of interspecies differential expression is a can of >>>> worms. >>>> Even if you adjust for gene length, there will still be differences in >>>> gc >>>> content and mappability between the species. >>>> >>>> Gordon >>>> >>>> >>>> On Wed, 27 Aug 2014, assaf www wrote: >>>> >>>> Dear Gordon thanks, >>>> >>>>> >>>>> Suppose I start with the following matrices: >>>>> >>>>> # 'counts' is the Rsem filtered counts >>>>> >>>>> counts[1:4,] >>>>>> >>>>>> h0 h1 h2 n0 n1 n2 >>>>> ENSRNOG00000000021 36 17 20 10 25 38 >>>>> ENSRNOG00000000024 1283 615 731 644 807 991 >>>>> ENSRNOG00000000028 26 12 11 18 23 28 >>>>> ENSRNOG00000000029 22 13 12 16 17 15 >>>>> >>>>> # 'geneLength' is the species-specific gene lengths, for species 'h' >>>>> and >>>>> 'n': >>>>> >>>>> geneLength[1:3,] >>>>>> >>>>>> h0.length h1.length h2.length n0.length n1.length >>>>> n2.length >>>>> ENSRNOG00000000021 1200 1200 1200 1303 1303 >>>>> 1303 >>>>> ENSRNOG00000000024 1050 1050 1050 3080 3080 >>>>> 3080 >>>>> ENSRNOG00000000028 1047 1047 1047 1121 1121 >>>>> 1121 >>>>> >>>>> >>>>> does the following code look correct, and may allow allows across >>>>> species >>>>> analysis ?: >>>>> (technically it works, I checked) >>>>> >>>>> # quantile normalization: (as in here: >>>>> http://davetang.org/wiki/tiki-index.php?page=Analysing+ >>>>> digital+gene+expression >>>>> ) >>>>> >>>>> x1 = counts*1000/geneLength >>>>> library(limma) >>>>> x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") >>>>> offset = log(counts+0.1)-log(x2+0.1) >>>>> >>>>> ... >>>>> >>>>> y <- estimateGLMCommonDisp(y,design,offset=offset) >>>>> y <- estimateGLMTrendedDisp(y,design,offset=offset) >>>>> y <- estimateGLMTagwiseDisp(y,design,offset=offset) >>>>> fit <- glmFit(y,design,offset=offset) >>>>> >>>>> ... >>>>> >>>>> >>>>> Thanks in advance for any help.., >>>>> Assaf >>>>> >>>> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________________________________________________ >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 3.2 years ago by assaf www140
Looking at the code for rpkm, it looks like it should work just fine for a matrix or a vector. On Wed Aug 27 09:30:11 2014, assaf www wrote: > Sorry I'm not clear: > for getting the FPKMs, I guess I only need to: > rpkm(y, gene.length=geneLength, normalized.lib.sizes=T, log=F) > > But gene.length should here be a vector, while in this case its a matrix. > > > Assaf > > > On Wed, Aug 27, 2014 at 6:14 PM, assaf www <assafwww at="" gmail.com=""> wrote: > >> This is very helpful for me, thanks. >> >> A slight change that I made in the code you sent, to avoid some R erros, >> is >> >> # to replace: >> offset = offset + gl >> # with: >> offset = sweep(gl,2,offset,"+") >> >> In addition to differential expression tests, I wanted also to extract >> FPKMs values (and/or normalized CPM values), that would take into account >> all components of the offset (which if I'm not mistaken are: library_size + >> TMM + gene_size). >> I assume rpkm()/cpm() should correct only for library_size + TMM. >> Is there a possibly "decent" solution for that ? >> >> all the best, and thanks, >> Assaf >> >> >> >> On Wed, Aug 27, 2014 at 4:45 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: >> >>> It works something like this: >>> >>> library(edgeR) >>> y <- DGEList(counts=counts) >>> y <- calcNormFactors(y) >>> >>> # Column correct log gene lengths >>> # Columns of gl should add to zero >>> >>> gl <- log(geneLength) >>> gl <- t(t(gl)-colMeans(gl)) >>> >>> # Combine library sizes, norm factors and gene lengths: >>> >>> offset <- expandAsMatrix(getOffset(y)) >>> offset <- offset + gl >>> >>> Then >>> >>> y$offset <- offset >>> y <- estimateGLMCommonDisp(y,design) >>> >>> etc. >>> >>> Note that I have not tried this myself. It should work in principle from >>> a differential expression point of view. >>> >>> On the other hand, there may be side effects regarding dispersion trend >>> estimation -- I do not have time to explore this. >>> >>> Gordon >>> >>> --------------------------------------------- >>> Professor Gordon K Smyth, >>> Bioinformatics Division, >>> Walter and Eliza Hall Institute of Medical Research, >>> 1G Royal Parade, Parkville, Vic 3052, Australia. >>> http://www.statsci.org/smyth >>> >>> On Wed, 27 Aug 2014, assaf www wrote: >>> >>> Probably wrong, but the reason I thought of using quantile normalization >>>> is >>>> the need to correct both for the species-length, and library size. >>>> >>>> >>>> On Wed, Aug 27, 2014 at 2:40 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> >>>> wrote: >>>> >>>> That doesn't look helpful to me. I suggested that you incorporate gene >>>>> lengths into the offsets, not do quantile normalization of cpms. >>>>> >>>>> Sorry, I just don't have time to develop a code example for you. I hope >>>>> someone else will help. >>>>> >>>>> The whole topic of interspecies differential expression is a can of >>>>> worms. >>>>> Even if you adjust for gene length, there will still be differences in >>>>> gc >>>>> content and mappability between the species. >>>>> >>>>> Gordon >>>>> >>>>> >>>>> On Wed, 27 Aug 2014, assaf www wrote: >>>>> >>>>> Dear Gordon thanks, >>>>> >>>>>> >>>>>> Suppose I start with the following matrices: >>>>>> >>>>>> # 'counts' is the Rsem filtered counts >>>>>> >>>>>> counts[1:4,] >>>>>>> >>>>>>> h0 h1 h2 n0 n1 n2 >>>>>> ENSRNOG00000000021 36 17 20 10 25 38 >>>>>> ENSRNOG00000000024 1283 615 731 644 807 991 >>>>>> ENSRNOG00000000028 26 12 11 18 23 28 >>>>>> ENSRNOG00000000029 22 13 12 16 17 15 >>>>>> >>>>>> # 'geneLength' is the species-specific gene lengths, for species 'h' >>>>>> and >>>>>> 'n': >>>>>> >>>>>> geneLength[1:3,] >>>>>>> >>>>>>> h0.length h1.length h2.length n0.length n1.length >>>>>> n2.length >>>>>> ENSRNOG00000000021 1200 1200 1200 1303 1303 >>>>>> 1303 >>>>>> ENSRNOG00000000024 1050 1050 1050 3080 3080 >>>>>> 3080 >>>>>> ENSRNOG00000000028 1047 1047 1047 1121 1121 >>>>>> 1121 >>>>>> >>>>>> >>>>>> does the following code look correct, and may allow allows across >>>>>> species >>>>>> analysis ?: >>>>>> (technically it works, I checked) >>>>>> >>>>>> # quantile normalization: (as in here: >>>>>> http://davetang.org/wiki/tiki-index.php?page=Analysing+ >>>>>> digital+gene+expression >>>>>> ) >>>>>> >>>>>> x1 = counts*1000/geneLength >>>>>> library(limma) >>>>>> x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") >>>>>> offset = log(counts+0.1)-log(x2+0.1) >>>>>> >>>>>> ... >>>>>> >>>>>> y <- estimateGLMCommonDisp(y,design,offset=offset) >>>>>> y <- estimateGLMTrendedDisp(y,design,offset=offset) >>>>>> y <- estimateGLMTagwiseDisp(y,design,offset=offset) >>>>>> fit <- glmFit(y,design,offset=offset) >>>>>> >>>>>> ... >>>>>> >>>>>> >>>>>> Thanks in advance for any help.., >>>>>> Assaf >>>>>> >>>>> >>> ______________________________________________________________________ >>> The information in this email is confidential and intended solely for the >>> addressee. >>> You must not disclose, forward, print or use it without the permission of >>> the sender. >>> ______________________________________________________________________ >>> >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 3.2 years ago by Ryan C. Thompson6.1k
Thanks Ryan, it seems you are correct On Wed, Aug 27, 2014 at 7:39 PM, Ryan <rct at="" thompsonclan.org=""> wrote: > Looking at the code for rpkm, it looks like it should work just fine for a > matrix or a vector. > > On Wed Aug 27 09:30:11 2014, assaf www wrote: > >> Sorry I'm not clear: >> for getting the FPKMs, I guess I only need to: >> rpkm(y, gene.length=geneLength, normalized.lib.sizes=T, log=F) >> >> But gene.length should here be a vector, while in this case its a matrix. >> >> >> Assaf >> >> >> On Wed, Aug 27, 2014 at 6:14 PM, assaf www <assafwww at="" gmail.com=""> wrote: >> >> This is very helpful for me, thanks. >>> >>> A slight change that I made in the code you sent, to avoid some R erros, >>> is >>> >>> # to replace: >>> offset = offset + gl >>> # with: >>> offset = sweep(gl,2,offset,"+") >>> >>> In addition to differential expression tests, I wanted also to extract >>> FPKMs values (and/or normalized CPM values), that would take into account >>> all components of the offset (which if I'm not mistaken are: >>> library_size + >>> TMM + gene_size). >>> I assume rpkm()/cpm() should correct only for library_size + TMM. >>> Is there a possibly "decent" solution for that ? >>> >>> all the best, and thanks, >>> Assaf >>> >>> >>> >>> On Wed, Aug 27, 2014 at 4:45 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> >>> wrote: >>> >>> It works something like this: >>>> >>>> library(edgeR) >>>> y <- DGEList(counts=counts) >>>> y <- calcNormFactors(y) >>>> >>>> # Column correct log gene lengths >>>> # Columns of gl should add to zero >>>> >>>> gl <- log(geneLength) >>>> gl <- t(t(gl)-colMeans(gl)) >>>> >>>> # Combine library sizes, norm factors and gene lengths: >>>> >>>> offset <- expandAsMatrix(getOffset(y)) >>>> offset <- offset + gl >>>> >>>> Then >>>> >>>> y$offset <- offset >>>> y <- estimateGLMCommonDisp(y,design) >>>> >>>> etc. >>>> >>>> Note that I have not tried this myself. It should work in principle >>>> from >>>> a differential expression point of view. >>>> >>>> On the other hand, there may be side effects regarding dispersion trend >>>> estimation -- I do not have time to explore this. >>>> >>>> Gordon >>>> >>>> --------------------------------------------- >>>> Professor Gordon K Smyth, >>>> Bioinformatics Division, >>>> Walter and Eliza Hall Institute of Medical Research, >>>> 1G Royal Parade, Parkville, Vic 3052, Australia. >>>> http://www.statsci.org/smyth >>>> >>>> On Wed, 27 Aug 2014, assaf www wrote: >>>> >>>> Probably wrong, but the reason I thought of using quantile >>>> normalization >>>> >>>>> is >>>>> the need to correct both for the species-length, and library size. >>>>> >>>>> >>>>> On Wed, Aug 27, 2014 at 2:40 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> >>>>> wrote: >>>>> >>>>> That doesn't look helpful to me. I suggested that you incorporate >>>>> gene >>>>> >>>>>> lengths into the offsets, not do quantile normalization of cpms. >>>>>> >>>>>> Sorry, I just don't have time to develop a code example for you. I >>>>>> hope >>>>>> someone else will help. >>>>>> >>>>>> The whole topic of interspecies differential expression is a can of >>>>>> worms. >>>>>> Even if you adjust for gene length, there will still be differences in >>>>>> gc >>>>>> content and mappability between the species. >>>>>> >>>>>> Gordon >>>>>> >>>>>> >>>>>> On Wed, 27 Aug 2014, assaf www wrote: >>>>>> >>>>>> Dear Gordon thanks, >>>>>> >>>>>> >>>>>>> Suppose I start with the following matrices: >>>>>>> >>>>>>> # 'counts' is the Rsem filtered counts >>>>>>> >>>>>>> counts[1:4,] >>>>>>> >>>>>>>> >>>>>>>> h0 h1 h2 n0 n1 n2 >>>>>>>> >>>>>>> ENSRNOG00000000021 36 17 20 10 25 38 >>>>>>> ENSRNOG00000000024 1283 615 731 644 807 991 >>>>>>> ENSRNOG00000000028 26 12 11 18 23 28 >>>>>>> ENSRNOG00000000029 22 13 12 16 17 15 >>>>>>> >>>>>>> # 'geneLength' is the species-specific gene lengths, for species 'h' >>>>>>> and >>>>>>> 'n': >>>>>>> >>>>>>> geneLength[1:3,] >>>>>>> >>>>>>>> >>>>>>>> h0.length h1.length h2.length n0.length >>>>>>>> n1.length >>>>>>>> >>>>>>> n2.length >>>>>>> ENSRNOG00000000021 1200 1200 1200 1303 1303 >>>>>>> 1303 >>>>>>> ENSRNOG00000000024 1050 1050 1050 3080 3080 >>>>>>> 3080 >>>>>>> ENSRNOG00000000028 1047 1047 1047 1121 1121 >>>>>>> 1121 >>>>>>> >>>>>>> >>>>>>> does the following code look correct, and may allow allows across >>>>>>> species >>>>>>> analysis ?: >>>>>>> (technically it works, I checked) >>>>>>> >>>>>>> # quantile normalization: (as in here: >>>>>>> http://davetang.org/wiki/tiki-index.php?page=Analysing+ >>>>>>> digital+gene+expression >>>>>>> ) >>>>>>> >>>>>>> x1 = counts*1000/geneLength >>>>>>> library(limma) >>>>>>> x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") >>>>>>> offset = log(counts+0.1)-log(x2+0.1) >>>>>>> >>>>>>> ... >>>>>>> >>>>>>> y <- estimateGLMCommonDisp(y,design,offset=offset) >>>>>>> y <- estimateGLMTrendedDisp(y,design,offset=offset) >>>>>>> y <- estimateGLMTagwiseDisp(y,design,offset=offset) >>>>>>> fit <- glmFit(y,design,offset=offset) >>>>>>> >>>>>>> ... >>>>>>> >>>>>>> >>>>>>> Thanks in advance for any help.., >>>>>>> Assaf >>>>>>> >>>>>>> >>>>>> ____________________________________________________________ >>>> __________ >>>> The information in this email is confidential and intended solely for >>>> the >>>> addressee. >>>> You must not disclose, forward, print or use it without the permission >>>> of >>>> the sender. >>>> ______________________________________________________________________ >>>> >>>> >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> > [[alternative HTML version deleted]]
ADD REPLYlink written 3.2 years ago by assaf www140
The code should have been: offset <- expandAsMatrix(getOffset(y),dim(y)) offset <- offset + gl This should give same result as your code. rpkm() corrects for gene length as well as library size -- that's the whole purpose of RPKMs: rpkm(y, gene.length=geneLength) should work for you without any modification. Gordon On Wed, 27 Aug 2014, assaf www wrote: > This is very helpful for me, thanks. > > A slight change that I made in the code you sent, to avoid some R erros, is > > # to replace: > offset = offset + gl > # with: > offset = sweep(gl,2,offset,"+") > > In addition to differential expression tests, I wanted also to extract > FPKMs values (and/or normalized CPM values), that would take into account > all components of the offset (which if I'm not mistaken are: library_size + > TMM + gene_size). > I assume rpkm()/cpm() should correct only for library_size + TMM. > Is there a possibly "decent" solution for that ? > > all the best, and thanks, > Assaf > > > > On Wed, Aug 27, 2014 at 4:45 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > >> It works something like this: >> >> library(edgeR) >> y <- DGEList(counts=counts) >> y <- calcNormFactors(y) >> >> # Column correct log gene lengths >> # Columns of gl should add to zero >> >> gl <- log(geneLength) >> gl <- t(t(gl)-colMeans(gl)) >> >> # Combine library sizes, norm factors and gene lengths: >> >> offset <- expandAsMatrix(getOffset(y)) >> offset <- offset + gl >> >> Then >> >> y$offset <- offset >> y <- estimateGLMCommonDisp(y,design) >> >> etc. >> >> Note that I have not tried this myself. It should work in principle from >> a differential expression point of view. >> >> On the other hand, there may be side effects regarding dispersion trend >> estimation -- I do not have time to explore this. >> >> Gordon >> >> --------------------------------------------- >> Professor Gordon K Smyth, >> Bioinformatics Division, >> Walter and Eliza Hall Institute of Medical Research, >> 1G Royal Parade, Parkville, Vic 3052, Australia. >> http://www.statsci.org/smyth >> >> On Wed, 27 Aug 2014, assaf www wrote: >> >> Probably wrong, but the reason I thought of using quantile normalization >>> is >>> the need to correct both for the species-length, and library size. >>> >>> >>> On Wed, Aug 27, 2014 at 2:40 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> >>> wrote: >>> >>> That doesn't look helpful to me. I suggested that you incorporate gene >>>> lengths into the offsets, not do quantile normalization of cpms. >>>> >>>> Sorry, I just don't have time to develop a code example for you. I hope >>>> someone else will help. >>>> >>>> The whole topic of interspecies differential expression is a can of >>>> worms. >>>> Even if you adjust for gene length, there will still be differences in gc >>>> content and mappability between the species. >>>> >>>> Gordon >>>> >>>> >>>> On Wed, 27 Aug 2014, assaf www wrote: >>>> >>>> Dear Gordon thanks, >>>> >>>>> >>>>> Suppose I start with the following matrices: >>>>> >>>>> # 'counts' is the Rsem filtered counts >>>>> >>>>> counts[1:4,] >>>>>> >>>>>> h0 h1 h2 n0 n1 n2 >>>>> ENSRNOG00000000021 36 17 20 10 25 38 >>>>> ENSRNOG00000000024 1283 615 731 644 807 991 >>>>> ENSRNOG00000000028 26 12 11 18 23 28 >>>>> ENSRNOG00000000029 22 13 12 16 17 15 >>>>> >>>>> # 'geneLength' is the species-specific gene lengths, for species 'h' and >>>>> 'n': >>>>> >>>>> geneLength[1:3,] >>>>>> >>>>>> h0.length h1.length h2.length n0.length n1.length >>>>> n2.length >>>>> ENSRNOG00000000021 1200 1200 1200 1303 1303 >>>>> 1303 >>>>> ENSRNOG00000000024 1050 1050 1050 3080 3080 >>>>> 3080 >>>>> ENSRNOG00000000028 1047 1047 1047 1121 1121 >>>>> 1121 >>>>> >>>>> >>>>> does the following code look correct, and may allow allows across >>>>> species >>>>> analysis ?: >>>>> (technically it works, I checked) >>>>> >>>>> # quantile normalization: (as in here: >>>>> http://davetang.org/wiki/tiki-index.php?page=Analysing+ >>>>> digital+gene+expression >>>>> ) >>>>> >>>>> x1 = counts*1000/geneLength >>>>> library(limma) >>>>> x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") >>>>> offset = log(counts+0.1)-log(x2+0.1) >>>>> >>>>> ... >>>>> >>>>> y <- estimateGLMCommonDisp(y,design,offset=offset) >>>>> y <- estimateGLMTrendedDisp(y,design,offset=offset) >>>>> y <- estimateGLMTagwiseDisp(y,design,offset=offset) >>>>> fit <- glmFit(y,design,offset=offset) >>>>> >>>>> ... >>>>> >>>>> >>>>> Thanks in advance for any help.., >>>>> Assaf >>>>> >>>> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________________________________________________ >> > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD REPLYlink written 3.2 years ago by Gordon Smyth32k
I checked, it's true, the results look the same. As for FPKM, of course you are right. Thanks a lot Assaf On Thu, Aug 28, 2014 at 2:47 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > The code should have been: > > offset <- expandAsMatrix(getOffset(y),dim(y)) > offset <- offset + gl > > This should give same result as your code. > > rpkm() corrects for gene length as well as library size -- that's the > whole purpose of RPKMs: > > rpkm(y, gene.length=geneLength) > > should work for you without any modification. > > Gordon > > > On Wed, 27 Aug 2014, assaf www wrote: > > This is very helpful for me, thanks. >> >> A slight change that I made in the code you sent, to avoid some R erros, >> is >> >> # to replace: >> offset = offset + gl >> # with: >> offset = sweep(gl,2,offset,"+") >> >> In addition to differential expression tests, I wanted also to extract >> FPKMs values (and/or normalized CPM values), that would take into account >> all components of the offset (which if I'm not mistaken are: library_size >> + >> TMM + gene_size). >> I assume rpkm()/cpm() should correct only for library_size + TMM. >> Is there a possibly "decent" solution for that ? >> >> all the best, and thanks, >> Assaf >> >> >> >> On Wed, Aug 27, 2014 at 4:45 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> >> wrote: >> >> It works something like this: >>> >>> library(edgeR) >>> y <- DGEList(counts=counts) >>> y <- calcNormFactors(y) >>> >>> # Column correct log gene lengths >>> # Columns of gl should add to zero >>> >>> gl <- log(geneLength) >>> gl <- t(t(gl)-colMeans(gl)) >>> >>> # Combine library sizes, norm factors and gene lengths: >>> >>> offset <- expandAsMatrix(getOffset(y)) >>> offset <- offset + gl >>> >>> Then >>> >>> y$offset <- offset >>> y <- estimateGLMCommonDisp(y,design) >>> >>> etc. >>> >>> Note that I have not tried this myself. It should work in principle from >>> a differential expression point of view. >>> >>> On the other hand, there may be side effects regarding dispersion trend >>> estimation -- I do not have time to explore this. >>> >>> Gordon >>> >>> --------------------------------------------- >>> Professor Gordon K Smyth, >>> Bioinformatics Division, >>> Walter and Eliza Hall Institute of Medical Research, >>> 1G Royal Parade, Parkville, Vic 3052, Australia. >>> http://www.statsci.org/smyth >>> >>> On Wed, 27 Aug 2014, assaf www wrote: >>> >>> Probably wrong, but the reason I thought of using quantile normalization >>> >>>> is >>>> the need to correct both for the species-length, and library size. >>>> >>>> >>>> On Wed, Aug 27, 2014 at 2:40 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> >>>> wrote: >>>> >>>> That doesn't look helpful to me. I suggested that you incorporate gene >>>> >>>>> lengths into the offsets, not do quantile normalization of cpms. >>>>> >>>>> Sorry, I just don't have time to develop a code example for you. I >>>>> hope >>>>> someone else will help. >>>>> >>>>> The whole topic of interspecies differential expression is a can of >>>>> worms. >>>>> Even if you adjust for gene length, there will still be differences in >>>>> gc >>>>> content and mappability between the species. >>>>> >>>>> Gordon >>>>> >>>>> >>>>> On Wed, 27 Aug 2014, assaf www wrote: >>>>> >>>>> Dear Gordon thanks, >>>>> >>>>> >>>>>> Suppose I start with the following matrices: >>>>>> >>>>>> # 'counts' is the Rsem filtered counts >>>>>> >>>>>> counts[1:4,] >>>>>> >>>>>>> >>>>>>> h0 h1 h2 n0 n1 n2 >>>>>>> >>>>>> ENSRNOG00000000021 36 17 20 10 25 38 >>>>>> ENSRNOG00000000024 1283 615 731 644 807 991 >>>>>> ENSRNOG00000000028 26 12 11 18 23 28 >>>>>> ENSRNOG00000000029 22 13 12 16 17 15 >>>>>> >>>>>> # 'geneLength' is the species-specific gene lengths, for species 'h' >>>>>> and >>>>>> 'n': >>>>>> >>>>>> geneLength[1:3,] >>>>>> >>>>>>> >>>>>>> h0.length h1.length h2.length n0.length n1.length >>>>>>> >>>>>> n2.length >>>>>> ENSRNOG00000000021 1200 1200 1200 1303 1303 >>>>>> 1303 >>>>>> ENSRNOG00000000024 1050 1050 1050 3080 3080 >>>>>> 3080 >>>>>> ENSRNOG00000000028 1047 1047 1047 1121 1121 >>>>>> 1121 >>>>>> >>>>>> >>>>>> does the following code look correct, and may allow allows across >>>>>> species >>>>>> analysis ?: >>>>>> (technically it works, I checked) >>>>>> >>>>>> # quantile normalization: (as in here: >>>>>> http://davetang.org/wiki/tiki-index.php?page=Analysing+ >>>>>> digital+gene+expression >>>>>> ) >>>>>> >>>>>> x1 = counts*1000/geneLength >>>>>> library(limma) >>>>>> x2 = normalizeBetweenArrays(data.matrix(x1),method="quantile") >>>>>> offset = log(counts+0.1)-log(x2+0.1) >>>>>> >>>>>> ... >>>>>> >>>>>> y <- estimateGLMCommonDisp(y,design,offset=offset) >>>>>> y <- estimateGLMTrendedDisp(y,design,offset=offset) >>>>>> y <- estimateGLMTagwiseDisp(y,design,offset=offset) >>>>>> fit <- glmFit(y,design,offset=offset) >>>>>> >>>>>> ... >>>>>> >>>>>> >>>>>> Thanks in advance for any help.., >>>>>> Assaf >>>>>> >>>>>> >>>>> ____________________________________________________________ >>> __________ >>> The information in this email is confidential and intended solely for the >>> addressee. >>> You must not disclose, forward, print or use it without the permission of >>> the sender. >>> ______________________________________________________________________ >>> >>> >> > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:10}}
ADD REPLYlink written 3.2 years ago by assaf www140
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