Question

Do I have clustering by library size?

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pkachroo ▴ 10

@pkachroo-11576

Last seen 4.1 years ago

Hi,

I have a question regarding large differences in library size amongst my samples. These samples are from invivo animal infection experiment and some samples had to be resequenced to get enough reads. I do not have a case/infected and control/uninfected scenario in this experiment, they are just all infected samples. The range of library size in my experiment is 100,000 to 81 million. I generated a PCA plot and colored them by the sequencing depth and wanted to check with the experts if this seems to be a case wherein samples with similar sequencing depth are clustering together? Also, I tried filtering genes that have 0 reads for >50% of the samples and replotted PCA, but it looked exactly the same.

Greatly appreciate help in this regard.

PCA plot

PCA DESeq2 Normalization librarysize • 2.2k views

ADD COMMENT • link updated 4.1 years ago by Michael Love 43k • written 4.1 years ago by pkachroo ▴ 10

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To me it doesn't look like it. Couple of notes though: (i) if you end up doing any sort of differential expression analysis, you might want to add the sequencing batch of the libraries as a control (and colour those in a separate PCA) to exclude batch effects, if any exists; (ii) the range of library sizes is quite large. You might need to take special care when analysing.

ADD REPLY • link 4.1 years ago António Miguel de Jesus Domingues ▴ 510

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Thank you Antonio for your suggestions. Greatly appreciate it.

ADD REPLY • link 4.1 years ago pkachroo ▴ 10

score 0 · Answer 1 · 2020-11-02

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Michael Love 43k

@mikelove

Last seen 3 days ago

United States

I don't think there is too much clustering by library size, but the one very highly sequenced sample may continue to drive PC1. You could see what happens if you down-sample that one.

This code will generate a new sample downsampling by p. For example, if you want to bring down the counts by 1/10 for sample j you would set p=.1.

new.cts <- rbinom( nrow(dds), prob=p, size=counts(dds)[ , j] )

Then you can do:

mode(new.cts) <- "integer"
counts(dds)[,j] <- new.cts

ADD COMMENT • link 4.1 years ago Michael Love 43k

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Thanks a lot, Micheal. Downsampling is a great idea. Thank you so much for the code, I will give it a try and report back.

ADD REPLY • link 4.1 years ago pkachroo ▴ 10

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I have regenerated the PCA after downsampling the sample "P7" by 1/3rd (to a similar sequencing depth as its replicate). I do not see any major improvement, what do you think? In our experiment, we had to resequence some samples as they were obtained from total RNA (host+pathogen) and we needed only the pathogen reads. Since pathogen accounted only for a small percentage, we had to resequence multiple samples to bump up the reads. In your opinion, how much variability in sequencing depth across samples is okay to have? enter image description here

ADD REPLY • link 4.1 years ago pkachroo ▴ 10

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Did you put P7 in twice? I would just replace the original P7 with the downsampled one.

ADD REPLY • link 4.1 years ago Michael Love 43k

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Apologize for the confusion. The 2 P7s on the PCA are biological replicates. I have updated the "before" and "after" downsampling PCAs to reflect the same. enter image description here

PCA plots

ADD REPLY • link 4.1 years ago pkachroo ▴ 10

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So then I agree that P7 is still driving PC1 to some extent.

ADD REPLY • link 4.1 years ago Michael Love 43k

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Indeed. Thanks a lot for the code. I have other datasets that may have the same issue with library size variation. Moving forward, in order to maintain consistency across datasets, how do I decide if downsampling is needed?
Look at the PCA's or should I look at the range and downsample all samples that exceed the minimum sequencing depth by a factor of 10? I am hoping to apply the same rule across the datasets as they will be presented in the same manuscript.

ADD REPLY • link 4.1 years ago pkachroo ▴ 10

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Hmm not sure if I have a hard and fast rule. I look at PCA and library size distribution for all datasets.

ADD REPLY • link 4.1 years ago Michael Love 43k