Hi all,

1_Why mapman does not show me the genes which are up or downregulated?
all of the genens are gray in different pathways.
I load my data in excell format, first column contains probe set names and their annotation ID besides, in next columns expression values in different time points during the experiment.
I am wondering if something is wrong with this kind of format.


2- I used of aglient microarray but when I choosed this for arabidopsis which is my plant, sometimes mapman tells me this is not the right mapping.
(But not always)!!!


Thanks in advance,
Vaji

Hi Vaji,

the problem you are describing "all of the genens are gray in different pathways" sounds like
the mapping you have chosen does not fit to the identifiers in your data file. To check this
have a look at the summary box that is shown on each pathway in the upper right corner. It
tells you which mapping was chosen, how many of the IDs in your data file could be mapped
using this mapping and how many of them are shown on the current pathway.

If you are working with AGILENT 44k chips for arabidopsis, the Ath_AGILENT mapping should,
in principle, work for you. You can download the mapping in text format and crosscheck whether
the IDs you are using in your data files are contained or somewhat modified (that would be a possible
reason why MapMan seems to be unable to recognize them). The text version of the mapping
is available here: http://mapman.gabipd.org/web/guest/mapmanstore

cheers,
Marc