Question: Some problems of creat DESeqDataSetFromMatrix step by DESeq2
0
gravatar for 1106518271
8 months ago by
110651827160
110651827160 wrote:

For this step:

dds < - DESeqDataSetFromMatrix(countData = counts,
                                  colData = coldata,
                                  design = ~condition)

I read a lot of examples on the website, but these examples seems for majority cases, here are three parts I couldn't make sure:

  1. countData = counts
    Generally, part of counts matrix like the following, conl1 conl2 are two samples,

                  conl1 conl2 rep1 rep2    
    ENSMUSGid1     0     0    3    4    
    ENSMUSGid2     0     1    0    0    
    ENSMUSGid3     0     1   10   12
    

    but for my data, even as for conl1, here are three experimental replications, so, it means, for colnames of my raw countData:
    conl1_1, conl1_2, conl1_3, conl2_1, conl2_2.... I plan just seem all of them(conl1_1, conl1_2, conl1_3) as conl. Is it okay?

  2. colData = coldata
    Can this coldata contains all potential variables I want to study, including cell type column, batch column, gender column, age column? And let design = ~condition1 + condition2 +condition3...(Order according to proportion from PCA)? Or study each variable one by one?

  3. design = ~condition
    Actually my colnames of raw countData also contains batch information, generally, people use design = ~condition, can I use design = ~batch + condition (I gave one column of batch for colData = coldata)? Or run a design = ~condition DEseq2 result then design = ~batch DEseq2 result? Or I should check batch effects exist firstly, then corrected, then do design = ~condition?

Thanks for your attention in advance, sorry for so many confused... Any ideas of each part will be very grateful!!!

rna-seq R • 228 views
ADD COMMENTlink modified 8 months ago by lakhujanivijay4.3k • written 8 months ago by 110651827160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1539 users visited in the last hour