how i can draw expression pattern of my interest genes expressed in a microarray?
i downloaded GSE63706 and normalized that by RMAExpress, now i have a text file (consisting of 13 columns and 22300 rows) of which i pasted a little bit in the below
Probesets GSM1555931_wp-a2.CE GSM1555883_cp-a2.CEL GSM1555884_cp-b1.CEL
AF506028_F_at 2.841923 3.343265 4.007341
Cit.100.1.S1_x_at 3.487702 3.405457 3.873674
i have also a list of probsets (a text file of my interest probsets) in this array like below
i am using these probes as hub in the array
i want to have a heat map showing the expression pattern of genes co-expressed with my interest probsets in this array, for example in this array i have 4 varieties and different tissues (rind and flesh) and phases (0,10,20,30,40 and 50 days after harvesting). heat maps showing the expression pattern of genes correlated with my probsets in varieties, tissues and phases separately.
i can produce co-expressed network using the hubs but i am intrested in tracking expression pattern of genes co-expressed with hubs in different organs, phases and varieties individually with heatmap or another way but i don't know how to do this.
please tell me something for inspiration
i tried to adapt my purpuse with github script like below but:
in R i changed directory and i typed so:
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
> data <- read.text("text1", comment.char="#")
Error: could not find function "read.text"