I am going to do in-silico analysis of several datasets (of GPL570 platform) but GEO datasets' Raw data are provided as supplementary file in .cel format, which I cannot open. I need to open them in Excel so I can select samples (from different datasets) that I will include and pre-process raw data for in my analyses later. Please help.
Hi, last time I used affymetrix microarray I input the data in Expression Console Software 1.4 and put the results in Transcriptome Analysis Console (TAC) Software 3.1 to get the p-values in comparison to my treatment groups.
If Im not mistaken the CEL data format has to be converted first using the expression console. Maybe u can ask the product specialist that u bought the microarray from to show you how to do this in detail. Hope it helps!
The first answer is one possibility; you have to install the software first. A second possibility with a much easier installation is using the RMAExpress tool of Bolstad (http://rmaexpress.bmbolstad.com/). You have to include CDF files of your Affymetrix chips first (defining the chip) and then you could include the CEL files. Once this is done you could normalize all your chips together and can output the normalized expression values. A third possibility is dChip (www.dchip.org). This is a little bit more complicated in analyzing the chips and you have a different normalization possibility.
Related to your query, I suggest you follow :: http://www.sthda.com/english/wiki/affymetrix-cel-files
https://www.researchgate.net/post/How_can_i_use_the_xxxCEL_files_microarray_raw_data_to_calculate_the_xxxxls_files_which_included_the_symbol_name_log_foldchange_and_P_value
AND: http://homer.ucsd.edu/homer/basicTutorial/affymetrix.html
Good Luck
- Badges
- Science topic
- Similar topics
- Filing