Question

how to get the estimated libSize in DiffBind

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Guandong Shang ▴ 40

@shangguandong1996-21805

Last seen 17 months ago

China

Hi, Dr Stark. In the Question: diffBind: differentially bound sites are highly different between using EDGER and DESEQ2. You mentioned

Correct, the factors are only estimated by DESeq2 if bFullLibrarySize=FALSE, otherwise they are based directly on the libSizes.

And I am wondering whether I can get the libSizes factor (full library size, total number of reads in BAM/SAM/BED file, instead of the peak count) in Diffbind project.

Best wishes Guandong Shang

diffbind • 1.0k views

ADD COMMENT • link updated 3.4 years ago by Rory Stark ★ 5.1k • written 3.9 years ago by Guandong Shang ▴ 40

score 1 · Answer 1 · 2020-06-01

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Rory Stark ★ 5.1k

@rory-stark-5741

Last seen 7 days ago

Cambridge, UK

data(tamoxifen_counts)
as.numeric(tamoxifen$class["Reads",])

[1] 776353 782419 438994 465700 577273 507493 1831766 747610 728601 804427 2918549

ADD COMMENT • link 3.9 years ago Rory Stark ★ 5.1k

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Thanks Dr.Stark. Sorry I just have another Question, I am wondering whether I can get the sizeFactors(according to the above libSize instead of peak count) , which will be assignd to DESeq2 dds when set bFullLibrarySize = TRUE.

Or I just calculate myself like below?

library(DiffBind)
data(tamoxifen_counts)
libSize <- as.numeric(tamoxifen$class["Reads",])

> libSize / max(libSize)
 [1] 0.2660065 0.2680849 0.1504152 0.1595656 0.1977945 0.1738854
 [7] 0.6276290 0.2561581 0.2496449 0.2756257 1.0000000

ADD REPLY • link 3.9 years ago Guandong Shang ▴ 40

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According to DiffBind Vignette,

If bFullLibrarySize is set to TRUE (default), then sizeFactors is called with the number of reads in the BAM/BED files for each ChIP sample, divided by the minimum of these;

Therefore, wouldn't it be, libSize/min(libSize) ?

ADD REPLY • link 3.9 years ago bioinfouser2 ▴ 10

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Thanks :) , I am sorry I did not see it.

ADD REPLY • link 3.9 years ago Guandong Shang ▴ 40

score 0 · Answer 2 · 2020-11-06

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Rory Stark ★ 5.1k

@rory-stark-5741

Last seen 7 days ago

Cambridge, UK

The recently released version of DiffBind includes a new interface function, dba.normalize(), that allows library sizes and normalization factors (or offsets) to be set and retrieved directly.

ADD COMMENT • link 3.4 years ago Rory Stark ★ 5.1k