Question: logfoldStandard Error and wald-statistics in DESeq2 results
0
gravatar for deena
4.5 years ago by
deena10
Germany
deena10 wrote:

Hi,

I am new to statitics and RNAseq analysis, I am using DESeq2 for the anaylzing the RNAseq data. I would like to know what lfcSE(logfoldchangeStandard Error) and stat (wald ) columns tries to convey. For an example. how can I interpret the following:

log2FC:-1.4; lfcSE: 0.144; stat:-10.13

Kindly guide me.

deseq2 wald • 9.7k views
ADD COMMENTlink modified 4.5 years ago by Michael Love25k • written 4.5 years ago by deena10
Answer: logfoldStandard Error and wald-statistics in DESeq2 results
0
gravatar for Michael Love
4.5 years ago by
Michael Love25k
United States
Michael Love25k wrote:

hi,

For information about the columns, read over the vignette:

vignette("DESeq2")

and the results man page:

?results

These both describe the columns.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Michael Love25k

Dear Michael,

Thanks for your quick response. By going throught he vignette, I undersatnd that smaller  the lfcSe more significant the effect of fold change? Am I right? What does that a value in wald statistic columns conveys.

Kindly guide me
 

ADD REPLYlink written 4.5 years ago by deena10
The Wald statistic is the LFC divided by its standard error. This Wald statistic is used to calculate p-values (it is compared to a standard normal distribution) . So it's the ratio of LFC and SE which determines significance.
ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by Michael Love25k

Thank you so much. Now I understood clearly. Also is the lesser the lfcSE, more singificant the log2fold change?

If basemean is the mean of normalized rowcounts, how log2foldchange is calculated.?

ADD REPLYlink written 4.5 years ago by deena10

hi Deena,

You should look over our paper, if you want details about the method:

http://genomebiology.com/2014/15/12/550

ADD REPLYlink written 4.5 years ago by Michael Love25k
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