Question: please help me to be clear about the up and down regulated genes from cuffdiff
0
gravatar for A
4.9 years ago by
A3.9k
A3.9k wrote:

Hi,

Supposing I have samples C1 and C2 evaluated by cuffdiff. from genes_exp.diff file I extracted 56 genes whose log2(fold-change) is negative and 122 genes whose log2(fold-change) is positive all statistically are significant.

This means 56 genes up regulated in sample C1 and 122 gene up regulated in sample C2????

Thank you

sequencing rna-seq myposts • 1.5k views
ADD COMMENTlink modified 2.4 years ago by _r_am32k • written 4.9 years ago by A3.9k
2
gravatar for iraun
4.9 years ago by
iraun3.8k
Norway
iraun3.8k wrote:

The genes_exp.diff file is a tab delimited file with the results of differential expression testing between samples (C1 and C2 in your case) for genes. The fold-change value is calculated using the following formula: log2(FPKMy/FPKMx), being x and y C1 and C2 in your case. So, the positive values in FC means upregulated genes for C2 sample in comparison with C1, and negative values are indicating a downregulated expression in C2 in comparison with C1. The FC is always a comparison between two conditions.

I hope to clarify things to you a little bit.

ADD COMMENTlink modified 2.4 years ago by _r_am32k • written 4.9 years ago by iraun3.8k

thank you, completely clear 

sorry I am right if I only used the significant ones (yes in column 14)????

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by A3.9k

Glad to help :)

ADD REPLYlink written 4.9 years ago by iraun3.8k
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