How to deal with these data with DESeq2 ?? In hurry!
1
1
Entering edit mode
alanzxr • 0
@alanzxr-11499
Last seen 7.5 years ago

Hey friend,

I was assigned to deal with these data, but I am new in R and RNASeq field,,,,I need your help!

Accession No. F_1 N_1 D_1 N_2 D_2 F_2
NM_001011874 7751 3036 13792 4453 13735 7540
NM_001195662 193 482 590 375 676 402
NM_011283 1191 1182 1193 820 1410 2186
NM_011441 18285 39633 8686 8828 2573 5512
NM_001289465 15403 33966 7119 7511 2274 5006

 

how to deal with them to get the following table?

Accession.No. F_1 N_1 D_1 N_2 D_2 F_2 D/N_logFC D/N_p.adj F/N_logFC F/N_p.adj
NM_001011874 8111.874739 2471.545754 7492.317342 6374.618315 14998.58678 10114.58605 1.262604558 0.001779481 1.05896152 0.010375656
NM_001195662 201.9857857 392.3863813 320.5095151 536.8250321 738.1903649 539.2657287 0.086864629 0.98567172 -0.213331555 0.889226854
NM_011283 1246.451144 962.2421217 648.0811042 1173.857404 1539.71659 2932.425082 -0.036936393 0.993557236 0.691838779 0.393448516
NM_011441 19136.32171 32264.41794 4718.551946 12637.57702 2809.709776 7394.111185 -2.318810515 5.13E-14 -0.714734691 0.059497094
NM_001289465 16120.14019 27651.02868 3867.300403 10752.24751 2483.2025 6715.333924 -2.31204868 7.63E-13 -0.685843883 0.090337235

 I just read about DESeq2 manual and know I should use normalization,,,,but I do not know how....I don't have that condition data the Professor said I do not need that....I wonder what can I do!!!

Great Thanks!

deseq2 normalization rnaseq • 1.1k views
ADD COMMENT
5
Entering edit mode
@mikelove
Last seen 10 hours ago
United States

This is not an appropriate post to the Bioconductor support site, which should be reserved for sincere questions about Bioconductor software not addressed by the documentation. The maintainers of Bioconductor software get emails when you post with the tag, and this is just post is essentially: "I want someone to show me step by step what to do, but I'm not willing to take the time to read the documentation or workflows."

I'd like to continue to be able to pay great attention to the emails I get from the Bioconductor support site and respond in a timely manner, but I will be less able and likely to do so if posts like this are showing up.

I'd recommend you post to a different site, such as https://www.biostars.org/

ADD COMMENT
0
Entering edit mode

"But first, read the manual/documentation."

ADD REPLY
0
Entering edit mode

Hi Mike,

Doesn't make it better, but the phenomenon is as old as the internet:

> library("fortunes")
> fortune(122)

I wish to perform brain surgery this afternoon at 4pm and don't know where to start. My background is the history of great statistician sports legends but I am willing to learn. I know there are courses and numerous books on brain surgery but I don't have the time for those. Please direct me to the appropriate HowTos, and be on standby for solving any problem I may encounter while in the operating room. Some of you might ask for specifics of the case, but that would require my following the posting guide and spending even more time than I am already taking to write this note.
   -- I. Ben Fooled (aka Frank Harrell)
      R-help (April 1, 2005)

 

ADD REPLY

Login before adding your answer.

Traffic: 810 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6