Question: tracking hub's targeted genes expression pattern in different conditions
0
gravatar for F
3.8 years ago by
F3.4k
Iran
F3.4k wrote:

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 probsets (a text file of my interest probsets) 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 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:

> 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"

 

heatmap hub co-expressing gene • 1.2k views
ADD COMMENTlink modified 3.7 years ago • written 3.8 years ago by F3.4k

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.

ADD REPLYlink written 3.8 years ago by PoGibas4.8k

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

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by F3.4k

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:

C: How To Draw A Heat Map For Gene Expression Data?C: To get genes for each clusters from heatmapC: Heat Map Using R- Based On PercentageC: Superimpose 2 HeatmapsC: Key With Heatmap 

ADD REPLYlink written 3.8 years ago by Sean Davis25k
1
gravatar for F
3.7 years ago by
F3.4k
Iran
F3.4k wrote:

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

ADD COMMENTlink written 3.7 years ago by F3.4k
1
gravatar for Sean Davis
3.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

You could try:

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

 

ADD COMMENTlink written 3.8 years ago by Sean Davis25k

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

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by F3.4k
1
gravatar for Alex Reynolds
3.8 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

Our Expression Atlas might offer you some inspiration.

ADD COMMENTlink written 3.8 years ago by Alex Reynolds28k

it does not work in plants

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by F3.4k
1

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.

ADD REPLYlink written 3.8 years ago by Alex Reynolds28k

thank you Alex

ADD REPLYlink written 3.8 years ago by F3.4k
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