Respected Dr. Michael Love

Dear Sir, Sir I have a Dataset of which I did mapping, and filtered out the genes, and then put it as an expression data in DESeq2, these are some problems I would like to address.

1. when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene names, and the even if I run it, it gives me only the number in front of the analysis and no name.

2. when i put in the raw data, directly from GEOquery, I am not able to map that Id's result in R back.

please guide me toward these problems I will be very thankful to you.

thank you Dev

directly from GEOquery

I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your question reproducible by putting data and code. Best to ask at biostars.org since this is a general question not suitable for the support site.