AffyExpress choose relative path folder
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@5de73a99
Last seen 8 months ago

I found quality report for affymetrix data using package AffyExpress quite complete and interesting. However, I was disappointed by the impossibility of choosing a relative folder where I could store the html ouput. Besides, if possible, it would be great to combine all png outputs into a single HTML document, if possible, instead of keeping them separated.


# include your problematic code here with any corresponding output 

AffyExpress::AffyQA(parameters = c("disease status:ch1"), raw= affybatch_microarray,Output = "GSE23117_QAReports.html") # working

 AffyExpress::AffyQA(parameters = c("disease status:ch1"), raw= affybatch_microarray,Output = "Control_Quality/GSE23117_QAReports.html") # not working, as not finding relative path of Control_Quality

AffyExpress::AffyQA(parameters = c("disease status:ch1"), raw= affybatch_microarray, Output= "/home/bncl_cb/rstudio/working/bmkanalysis/tests/testthat/Control_Quality/GSE23117_QAReports.html") # not working as well with absolute path

Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/tmp/RtmpgFiLen//home/bncl_cb/rstudio/working/bmkanalysis/tests/testthat/Control_Quality/GSE23117_QAReports.html.html': No such file or directory

Here's my sessionInfo: it would be great to both specify a filename in relative and absolute path, as being platform-independant using functions normalizePath and path.expand on R.

sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /softhpc/R/4.0.2/lib64/R/lib/libRblas.so
LAPACK: /softhpc/R/4.0.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] hgu133plus2cdf_2.18.0 bmkanalysis_1.0.0     simpleaffy_2.64.0     genefilter_1.72.0     affyPLM_1.64.0        preprocessCore_1.50.0
 [7] gcrma_2.60.0          affy_1.68.0           Biobase_2.48.0        BiocGenerics_0.36.0   R2HTML_2.3.2
folder quality QualityControl AffyExpress • 132 views
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