Question

Normalizing data (that is not in microarray "format")

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Emmanuel Levy ▴ 270

@emmanuel-levy-1240

Last seen 7.0 years ago

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

affy affy • 1.2k views

ADD COMMENT • link updated 16.0 years ago by Sean Davis 21k • written 16.0 years ago by Emmanuel Levy ▴ 270

score 0 · Answer 1 · 2008-12-06

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Sean Davis 21k

@sean-davis-490

Last seen 3 months ago

United States

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 COMMENT • link 16.0 years ago Sean Davis 21k

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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 REPLY • link 16.0 years ago Emmanuel Levy ▴ 270