[BioC] Minor problem with siggenes's command sam2excel when entrez=TRUE

Manca Marco (PATH) m.manca at path.unimaas.nl
Wed Jul 29 16:23:46 CEST 2009

Dear Holger and dear Bioconductors,

I am using siggenes to perform SAM on the dataset gse9820 (mainly replicating the elaboration described by the authors of the object). It works perfectly but when I am exporting my SAM output of interest to a .csv files it gives me an error message if I ask to add Entrez links to the output (entrez = TRUE). It works just fine if I omit this requeste:

> sam2excel(sam.out1, 0.4, "control_patient_diffExpr12.csv", excel.version=2, n.digits = 5, entrez = TRUE, what = "both", quote = FALSE)
Loading required package: annotate
Loading required package: AnnotationDbi
Error: getAnnMap: GPL6255.db package not attached and load is FALSE
Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA) : 
  error in evaluating the argument 'envir' in selecting a method for function 'mget'


> sam2excel(sam.out1, 0.4, "control_patient_diffExpr.csv", excel.version=2, n.digits = 5, what = "both", quote = FALSE)
Output is stored in control_patient_diffExpr.csv 

This is not a major issue, since I have already the Entrez ID ( NM_######.#)  instead of the Illumina ID on the output files:
> sam.out1 <- sam(gse, gse$characteristics_ch1, gene.names = fData(gse)$GB_ACC)

Yet I wonder if there's a way to make it work. I have tried preserving the Illumina ID (basically omitting the #gene.names = fData(gse)$GB_ACC# option from the sam command) along my analysis and then associating the sam output to an annotation database (through the #chip = "chipID"# option) in sam2excel but it didn't work, neither with "lluminaHumanv2BeadID" nor with "lumiHumanAll".

Where am I doing wrong? Thank you in advance.

Best regards, Marco

-----By the way, the following is my session info, just in case------
> sessionInfo()
R version 2.9.0 (2009-04-17) 


attached base packages:
[1] splines   stats     graphics  grDevices datasets  utils     methods  
[8] base     

other attached packages:
 [1] annotate_1.22.0     AnnotationDbi_1.6.1 GEOquery_2.8.0     
 [4] RCurl_0.98-1        bitops_1.0-4.1      affy_1.22.0        
 [7] siggenes_1.18.0     multtest_2.1.1      Biobase_2.4.1      
[10] rcom_2.2-1          rscproxy_1.3-1     

loaded via a namespace (and not attached):
[1] affyio_1.12.0        DBI_0.2-4            MASS_7.2-47         
[4] preprocessCore_1.6.0 RSQLite_0.7-1        survival_2.35-4     
[7] tools_2.9.0          xtable_1.5-5  


Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
E-mail: m.manca at path.unimaas.nl
Mobile: +31626441205
Twitter: @markomanka

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