Question: Problems using text to subset array information from anexpression set
gravatar for Alvord, Greg DMS [Contr]
13.6 years ago by
Alvord, Greg DMS [Contr]160 wrote:
Hi Jeff - I'm a rookie myself with Bioconductor and R (been at it a couple of weeks). It appears that > Data <- ReadAffy() > alldata <- rma(Data) alldata is now simply a an AffyBatch object. It is not a matrix or data frame. If you create an object > alldata.exprs <- exprs(alldata) you create a matrix, but still not a data frame. You still may have problems naming the rows and columns explicitly. Create a data frame, e.g., > alldata.exprs.df <- data.frame(alldata.exprs) creates a data frame. And then you can easily extract something like > alldata.exprs.df["1007_s_at',] or > alldata.exprs.df[,"AA100.CEL") I think. Hope this helps. As a newcomer I'm trying to extract objects from Bioconductor operations in objects like matrices and data frames that I'm more familiar with. HTH, Greg W. Gregory Alvord, Ph.D. Director, Statistical Consulting Services Computer and Statistical Services National Cancer Institute at Frederick Fort Detrick at 7th Street Post Office Box B Miller Drive, Building 362, Room 33 Frederick, MD 21702-1201 Phone: 301.846.5101 Fax: 301.846.6196 E-mail: gwa at -----Original Message----- From: [mailto:bioconductor-bounces at] On Behalf Of Jeff Lande Sent: Tuesday, April 04, 2006 2:16 PM To: bioconductor at Subject: [BioC] Problems using text to subset array information from anexpression set I have an odd problem that I cannot seem to figure out. I have a set of CEL files in a directory, which I read using the ReadAffy() command. Then I run the rma command to preprocess. > Data <- ReadAffy() > alldata <- rma(Data) I've done this many times before without problems. However, when I try to use text instead of numbers for subscripting, I get an error. For example, I am able to access data from the first row and column using numeric subscripts > alldata[1,1] Expression Set (exprSet) with 1 genes 1 samples phenoData object with 1 variables and 1 cases varLabels sample: arbitrary numbering but using text for either subscript, I get an error. > alldata["1007_s_at",] Error in alldata["1007_s_at", ] : no 'dimnames' attribute for array > alldata[,"AA100.CEL"] Error in alldata[, "AA100.CEL"] : no 'dimnames' attribute for array I actually went through what I think was the same process last week (and many times previously) and had no problems, so I'm stumped. Here is my session information: > sessionInfo() R version 2.1.0, 2005-04-18, ia64-unknown-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: hgu133acdf affy reposTools Biobase "1.4.3" "1.6.7" "1.5.19" "1.5.12" I must be missing something obvious, but I just can't figure out what is going wrong. Does anyone have insight into this problem? Jeff Lande Post-Doctoral Associate University of Minnesota _______________________________________________ Bioconductor mailing list Bioconductor at Search the archives:
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