Entering edit mode
7.6 years ago
rajasekargutha
▴
60
i am working on differential gene expression analysis on zebrafish datasets, i am working with GPL 14664 agilent platform but there is no annotation package available. i used limma package and i got results. but how to convert into gene symbols.
logFC t P.Value adj.P.Val B
16359 -1.074112554 -12.97837673 7.26E-10 6.31E-06 12.639771
2765 -0.863886429 -12.83268681 8.56E-10 6.31E-06 12.49513661
Annotations are available for this array and it contains gene symbols. Scroll down the page and click on download full table.
how to map the id number from the table
I don't understand the question. Annotation table has ID's and gene symbols in each row.
i doubt that they are not Agillent probe IDs and i am not finding any match from these ids in the table
If you used that "platform" (GPL14664) as defined by GEO then that annotation table is what you should be able to use.
Are you referring to (16359 and 2765) as ID's in the example you posted above? You must not have used the right array definition file somewhere along the way in that case. Is that possible?
i have run the code which is given in limma package and i didnt get even any error while performing analysis.
When a program runs and produces output without errors it does not equate to "this result must be right". It is hard to write good code that catches all edge use cases and as such it is not surprising that not all user errors get caught during program execution.
I assume your identifiers are Entrez IDs, and googling "convert entrez id to gene symbol" will give you lot's of ideas on how to solve this.
they are nor entrez ids neither agilent probe ids, then what ids these could be???