Question: DESEQ2 results - write to TSV file
0
gravatar for cpak1981
5 weeks ago by
cpak1981100
cpak1981100 wrote:

How can I write the values of Formal class 'DESeqResults' [package "DESeq2"] with 6 slots

log2 fold change (MAP): condition treat vs ctrl  
Wald test p-value: condition treat vs ctrl  
DataFrame with 15729 rows and 6 columns  
                   baseMean log2FoldChange      lfcSE      stat       pvalue  
                   <numeric>      <numeric>  <numeric> <numeric>    <numeric>  
A       302.12240     0.35943317 0.15667370  2.294151 2.178181e-02  
B       18.83989     0.20074213 0.29998407  0.669176 5.033832e-01  
C      5946.15326     0.07679007 0.05139921  1.493993 1.351774e-01  
D 6018.48179    -0.09557543 0.07490464 -1.275961 2.019692e-01  
E      7302.76778    -0.31757508 0.05084542 -6.245894 4.213826e-10  

to TSV file? Using readr::write_tsv gives an error

deseq2 • 173 views
ADD COMMENTlink written 5 weeks ago by cpak1981100
2
gravatar for venu
5 weeks ago by
venu5.3k
Germany
venu5.3k wrote:

Did you check DEseq 2 manual?

Exporting results to CSV files

ADD COMMENTlink written 5 weeks ago by venu5.3k

Thanks! - I looked through the manual but not the vignette - the solution is trivial

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by cpak1981100

What do you mean by trivial? Isn't the vignette/manual helpful? Can you post the commands you tried?

ADD REPLYlink written 5 weeks ago by venu5.3k
2

He's saying it's an easy solution - he just didn't know where to look.

ADD REPLYlink written 5 weeks ago by jared.andrews07750
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