converting probes robes to gene IDs

Question

[bioinformatics]

Hi,

I have performed differential expression analysis and have a excel file with p values.

Does anyone know how I might convert the probes to gene ID, so I know which genes were differentially expressed.

Thanks!

[ATpoint]

Google it or use the search function. As said before, these array questions have been asked extensively over the last decade. Show effort and find them.

[bioinformatics]

I have over 16,000 probe names which makes it difficult to google. Ok thanks, I will have a look.

[ATpoint]

Google for a thread explaining how to do automated lookup. That has been asked many tomes before. For sure don’t google each probe…c’mon.

[bioinformatics]

Did you also happen to know how to create a character vector in R with 16384 values?

[Kevin Blighe]

It should not be an issue?

vec <- paste0('var', 1:16384)
str(vec)
chr [1:16384] "var1" "var2" "var3" "var4" "var5" "var6" "var7" "var8" "var9" "var10" "var11" "var12" "var13" "var14" "var15" "var16" "var17" "var18" "var19" ...

[bioinformatics]

Ok thanks, I have a list of 16384 probe names in a text file that are unique and not sequential. Is there are way of converting this column/file to a character vector?

Answer 1

[Kevin Blighe]

I have answered you here: microarray analysis in R