Question

How to deal with these data with DESeq2 ?? In hurry!

1

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alanzxr • 0

@alanzxr-11499

Last seen 8.2 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 • 1.3k views

ADD COMMENT • link updated 8.2 years ago by Michael Love 43k • written 8.2 years ago by alanzxr • 0

score 5 · Answer 1 · 2016-09-20

5

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Michael Love 43k

@mikelove

Last seen 3 days 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 • link 8.2 years ago Michael Love 43k

0

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"But first, read the manual/documentation."

ADD REPLY • link 8.2 years ago WouterDeCoster ▴ 130

0

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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 • link 8.2 years ago Wolfgang Huber ★ 13k