HELP !!!

[Rohit Panchakshari]

Hello,

I need some help regarding making heat-maps with dCHIP.

I have uploaded multiple cDNA arrays data, but now I need to compare
select genes amongst them for their expression correlation and depict
it as a heat map diagram.

I would be grateful if anybody even just posts some relevant manual
link.

Impatiently waiting,
Thanks,
Rohit.

[Craig_Mullen]

After loading your arrays, normalizing, etc., click on Analysis
>>Clustering/enrichment.

In the dialog box that comes up enter the name of a text file that has
the probe set numbers and name of genes you are interested in making
the heat map.

Choose clustering options and click OK.

Craig Mullen

[Rohit Panchakshari]

@Craig : Thanks!

It worked !

I have two questions though:
1) This might be a very naive question so pardon me for that; while
choosing the genes of my interest I selected all the different probe
sets for a particular gene. Thus in my gene list file although I had
only 11 genes there are about 56 rows because of the different probe
sets on the array. I was hoping that DChip would somehow average all
the probe sets values for a particular gene, and thus represent only
one row for each gene in the heat map. But it doesn't.
How to get around this please?

2) Also I wanted to compare the expression of these particular genes
against one particular gene (miRNA) which I quantified using Q-PCR (I
have nomarlized numerical values for each sample).
Is there a way where I can have all this information in heat-map
diagram form?

I hope it looks some what like this:
Samples
A1 A2 A3 A4 A5
( Heat MAP ) miRNA
( Heat MAP ) Gene ABC
( Heat MAP ) Gene DEF
( Heat MAP ) Gene GHI
( Heat MAP ) Gene JKL

Thanks,
Rohit.

[Cheng Li]

Rohit,

1. dChip cannot average. You can check 'Tools-options-remove redundant
probe set' to use only unique genes for clustering.

2. You can export these genes' data at ' tools-export expression
values' , then modify the file to include the mirna data. Then read it
back using 'get external data' and do the rest analysis.

Cheng

在 Aug 21, 2009，1:34 PM，Rohit Panchakshari <rpanch...@gmail.com>
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