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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices datasets utils methods base other attached packages:  hgu133plus2cdf_2.18.0 bmkanalysis_1.0.0 simpleaffy_2.64.0 genefilter_1.72.0 affyPLM_1.64.0 preprocessCore_1.50.0  gcrma_2.60.0 affy_1.68.0 Biobase_2.48.0 BiocGenerics_0.36.0 R2HTML_2.3.2