I am working with affymetrix .cel files obtained from a Cytoscan HD array. In order to carry out an analysis in Bioconductor I am following the tutorial at
http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/
The trouble occurs with the .cdf available from Affymetrix which needs to be read as a package (Sorry to sound naive, I am doing this for the first time). I tried creating an environment following the post at How To Save A Cdf Environment In A File ? using arrayInitiative, which is used for changing the format of the .cdf file into one that can then be read by makecdfenv. ArrayInitiative also requires probe sequences which are available from Affymetrix as the file CytoScanHD_Array.probe_tab, about which ArrayInitiative complains for not having 6 columns as well as an incorrect header. Can I edit this probe_tab file to make it into 6 columns? (THe file has an extra column for perfect/mis match) Is there a .cdf for cytoscan HD available from bioconductor that I can use here? Or is there a completely different way of doing things? I appreciate any help to get around this. Thank you very much in advance.
Trying aroma.affymetrix next.
Used rCGH to analyze the CNVs. Easy to use. Theres also RawCopy, but I am sticking with rCGH. Moving on to the SNPs now.
Hi @arti.pandey69. Only for curiosity... how did you generate the
cychhp.txtfiles? Manually through Affymetrix software or by another R package? Thanks a lot!