Question: Normalizing data (that is not in microarray "format")
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gravatar for Emmanuel Levy
10.9 years ago by
Emmanuel Levy270
Emmanuel Levy270 wrote:
Dear All, I am trying to normalize data that looks like absolute mRNA expression values (although it's not). This means that I do not have an affy object. I' tried normalize.loess, which partially worked as it gave me the following warning (when I set missing values to 1 it disappears): 50: In means[, k] - aux ... : longer object length is not a multiple of shorter object length I'd like to use other methods (linear or non linear), but I've got a problem because I do not have an expression object. --> for example, maNorm doesn't work and I've got the following error: Error in slot(mnorm, "maNormCall") <- match.call() : object "mnorm" not found Any idea on which functions to use, or on how to "transform" my data.frame into an affy object would be great. Thanks, Emmanuel
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ADD COMMENTlink modified 10.9 years ago by Sean Davis21k • written 10.9 years ago by Emmanuel Levy270
Answer: Normalizing data (that is not in microarray "format")
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gravatar for Sean Davis
10.9 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Fri, Dec 5, 2008 at 10:08 PM, Emmanuel Levy <emmanuel.levy at="" gmail.com=""> wrote: > Dear All, > > I am trying to normalize data that looks like absolute mRNA expression > values (although it's not). > This means that I do not have an affy object. > > I' tried normalize.loess, which partially worked as it gave me the > following warning (when I set missing values to 1 it disappears): > > 50: In means[, k] - aux ... : > longer object length is not a multiple of shorter object length > > > I'd like to use other methods (linear or non linear), but I've got a > problem because I do not have an expression object. > --> for example, maNorm doesn't work and I've got the following error: > > Error in slot(mnorm, "maNormCall") <- match.call() : > object "mnorm" not found > > Any idea on which functions to use, or on how to "transform" my > data.frame into an affy object would be great. Hi, Emmanuel. Reading the help for normalize.loess, it appears that it takes a matrix as input. You do not need an affy object. Also, note that a data.frame is not a matrix. For any of the normalization methods that you might choose, it helps to read the help carefully, as that will tell you what types of data can be used; most normalization routines will take a matrix as input. If you need more specific help, you will need to post some reproducible example code and give the output of sessionInfo(). Sean
ADD COMMENTlink written 10.9 years ago by Sean Davis21k
Dear Sean, Thank you for your reply. > Reading the help for normalize.loess, it appears that it takes a > matrix as input. You do not need an affy object. Also, note that a This is actually why I tried to use normalize.loess. Although I get warnings, it does normalize my data. The following piece of code generates the error mentioned in my previous email: > my.mat = matrix(nrow=100, ncol=4, runif(400) ) > my.mat[1,1]=NA > my.mat.n = normalize.loess(my.mat) Warning messages: 1: In means[, j] + aux : longer object length is not a multiple of shorter object length I actually figured out that the NormalizeBetweenArray method from the Limma package does the simple "scaling" normalization I was looking for. Best, Emmanuel > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-pc-linux-gnu locale: LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GOstats_2.4.0 Category_2.4.0 genefilter_1.22.0 [4] survival_2.34-1 RBGL_1.16.0 annotate_1.20.1 [7] xtable_1.5-4 GO.db_2.2.0 AnnotationDbi_1.2.2 [10] RSQLite_0.6-9 DBI_0.2-4 graph_1.18.0 [13] marray_1.20.0 limma_2.16.3 YEAST_2.0.1 [16] affy_1.20.0 Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 cluster_1.11.11 preprocessCore_1.4.0 > data.frame is not a matrix. For any of the normalization methods that > you might choose, it helps to read the help carefully, as that will > tell you what types of data can be used; most normalization routines > will take a matrix as input. If you need more specific help, you will > need to post some reproducible example code and give the output of > sessionInfo(). > > Sean >
ADD REPLYlink written 10.9 years ago by Emmanuel Levy270
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