Question

ARACNE and TimeDelay ARACNE

1

Entering edit mode

9.1 years ago

ericadams.8810 ▴ 10

Hi,all!

I am trying to work with ARACNE and TimeDelay ARACNE for the first time, so I do not know in which format I have to import my data? who can give me an example?

Can anybody suggest me any solution?

Regards
Eric

RNA-Seq • 1.8k views

ADD COMMENT • link updated 19 months ago by Ram 43k • written 9.1 years ago by ericadams.8810 ▴ 10

Ram · Answer 1 · 2015-10-07

0

Entering edit mode

8.5 years ago

pengchy ▴ 450

Hi Eric,

How about your work now?

The input data format is pretty simple as the function documentation illustrated. In R, if you have the expression data in matrix, then transform it into Expression class using ExpressionSet function from Biobase.

I also have a question about TDARACNE: what is the maximum genes it can treat? Currently, I have tested a 546 genes across 6 time points, 42 minutes passed and still running. I wonder if it possible to run this program using multiple CPUs?

Best,
Pengcheng

ADD COMMENT • link updated 19 months ago by Ram 43k • written 8.5 years ago by pengchy ▴ 450

0

Entering edit mode

From the TDARCNE paper, currently this package only support little-medium networks. How many genes are called little-medium network? The maximum genes number tested in the paper is 30.

ADD REPLY • link updated 19 months ago by Ram 43k • written 8.5 years ago by pengchy ▴ 450

0

Entering edit mode

Hi pengchy,

I noted that the matrix of the expression is based on one sample: gene on the rows and time points on the columns. What should I do if I have multiple samples at time series?

Best,
Gang Xue

ADD REPLY • link updated 19 months ago by Ram 43k • written 3.6 years ago by Gang Xue • 0