tracking hub's targeted genes expression pattern in different conditions

Question

[zizigolu]

Hello,

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 probesets (a text file of my interest probesets) in this array like below

Cit.13168.1.S1_at,Cit.29783.1.S1_at,Cit.29783.1.S1_s_at,Cit.30289.1.S1_at

I am using these probes as hub in the array

I want to have a heatmap showing the expression pattern of genes co-expressed with my interest probesets 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). Heatmaps showing the expression pattern of genes correlated with my probesets in varieties, tissues and phases separately.

I can produce co-expressed network using the hubs but I am interested 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 purpose with github script like below but:

In R I changed directory and I typed so:

> library(gplots)
Attaching package: 'gplots'

The following object is masked from 'package:stats':

lowess

> library(RColorBrewer)
> data <- read.text("text1", comment.char="#")
Error: could not find function "read.text"

[PoGibas]

Sarah, instead of copy/pasting same comment, can you please update this question and post example data. How does normalised text file look like? How does list of probes look like? This is the only why we can help you to read it into R and plot it.

[zizigolu]

yes you all right, i will do so hoping to solve my problem

[Sean Davis]

I suspect that the question that you ask here is related to the question you asked here: expression pattern (heat map) of a list of probsets ids

And also to the identical comments you left on these posts:

• Key With Heatmap
• Superimpose 2 Heatmaps
• Heat Map Using R- Based On Percentage
• To get genes for each clusters from heatmap
• How To Draw A Heat Map For Gene Expression Data?

Answer 1

[zizigolu]

hey Sarah use color mosaic which will save you from R in this case but try to learn R if you could!

Answer 2

[Sean Davis]

You could try:

• heatmaps
• parallel coordinate plots
• barplots (one per gene)

[zizigolu]

I tried to work with heatmap in R but I am fully confused now. Why you don't help me Sean? :(

Answer 3

[Alex Reynolds]

Our Expression Atlas might offer you some inspiration.

[zizigolu]

it does not work in plants

[Alex Reynolds]

That's correct, we do not offer expression data for other species. However, it might give you some ideas how to visualize your data for your experiment and tissues/organs.

[zizigolu]

thank you Alex