ialbert
commented
5 months ago I am afraid that tool has kind of gone obsolete. I used to rely on it quite a bit in the past, but in the past few years I have not used it all - so I don't even know whether it still works.
Sounds like it is not working anymore.
I will investigate the matter tomorrow, but it is likely that I will remove this chapter from the book.
When I learn the chapter gene ontology-Using the ErmineJ tool
Files downloaded by below two codes are broken.
curl -O http://chibi.ubc.ca/microannots/Generic_human_noParents.an.txt.gzcurl -O http://chibi.ubc.ca/microannots/Generic_mouse_noParents.an.txt.gzTherefore, I tried to download annotation file from website directly. But when I loaded the annotation file I download (Generic_human_noParents.an.txt.gz) in ErmineJ 3.2 on Windows 10, an error occurred. Error: Gene annotation reading error during initialization: there are no gene sets Check the file format. Besides, I also checked the content of annotation file and found that there is no GO annotation in this annotation file. Generic_human.an.txt.gz is in the same situation.
Therefore, I changed to load another annotation file (BTS.an.txt.gz, Generic_human_ncbiIds_noParents.an.txt.gz) and succeed. But when I start ORA analysis and load gene score file, software didn't find any valid gene. And the gene offered by gene score file exist in these two annotation files.
I found that the first column and the second column are the same in Generic_human_noParents.an.txt.gz and Generic_human.an.txt.gz, but they are not same in BTS.an.txt.gz and Generic_human_ncbiIds_noParents.an.txt.gz. Therefore, I copied the second column content and paste to the first column in BTS.an.txt.gz and Generic_human_ncbiIds_noParents.an.txt.gz.
Finally, software found the valid gene from gene score file.
I don't know what happened here. And Does ErmineJ search the gene from gene score file based on the first column of annotation file? When the first column of annotation file is some number, do I need to change the number to gene name?