Tutorial: Clustering and results Display from PART II (PART III) - MeV software version
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3.3 years ago by
majuang6690
majuang6690 wrote:

PART I - From Data import to Normalization in Microarray Analysis using in R (Part I)

PART II - From Genefiltering to Results storgae in Microarray Analysis using in R (Part II) - FARMS

I prepared the data from PART II. I think that data presentation is important for understanding the results in large data. I display clustering results through MeV software (free). From PART II, I selected 212 genes using FARMS and genefiltering (Standard Deviation) at GSE4536 data.

Open MeV software (version 4.9 - http://www.tm4.org/mev.html)

File -> Load Data -> Single-color Array select -> mydata_GSE4536_xxx_xxx.txt. text file upload

Load Annotation Data -> Automatically download -> Homo sapiens -> hgu133plus2

Expression Table -> first row x first column values click -> Load Click!

Clustering Click -> Hierarchial Clustering (HC) -> Tree Selection (check Gene Tree and Sample Tree) ->

Distance Metric Selection (Current Metric -> Euclidean Distance) -> Linkage Method (Complete linkage clustering) -> OK click!! Hierarchial Clustering. Samples are divided into two groups. one group (green) contains serum-cultured differentiated glioma stem cells and traditional glioma cell lines and another (blue) includes serum free-cultured glioma stem cells and patient tissues

For identifying significant genes between groups, I perform statistics, SAM analysis.

Statistics click -> Significance Analysis of Microarrays (SAMs) click -> Two-class unpaired -> Cluster Selection (green - Group 1, blue - Group 2) -> check HC -> Tree Selection (check Gene Tree and Sample Tree) ->

Distance Metric Selection (Current Metric -> Euclidean Distance) -> Linkage Method (Complete linkage clustering) -> OK click!!

We will show SAM graph and HC as below

SAM graph. SAM graph shows up-regulated or down-regulated genes between two groups HC from SAM results

Next, I usually organize top gene list through Excel.

enter image description here

tutorial R gene • 1.4k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by majuang6690

Use the "tutorial" category for these guides.

It would also be useful to provide links for previous part in series (at the top of this post) and next part (at end, if there is one).

ADD REPLYlink written 3.3 years ago by genomax73k
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