Error in shrinkage for DESeq2
1
0
Entering edit mode
Kent • 0
@5f50f52d
Last seen 7 days ago
United Kingdom

Hi I have done a DESeq2 DGE analysis and it showed an error when I was using ashr shrinkage

using 'ashr' for LFC shrinkage. If used in published research, please cite:
    Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
    https://doi.org/10.1093/biostatistics/kxw041

warning: solve(): system is singular (rcond: 4.52254e-18); attempting approx solution

warning: solve(): system is singular (rcond: 7.84057e-18); attempting approx solution

warning: solve(): system is singular (rcond: 3.78635e-19); attempting approx solution

warning: solve(): system is singular (rcond: 6.26207e-19); attempting approx solution

warning: solve(): system is singular (rcond: 7.78489e-19); attempting approx solution

warning: solve(): system is singular (rcond: 1.14601e-18); attempting approx solution

I assume that stems from co-linearity of some of the factors? Is there any fix? May I ask if the result is trustworthy? And if I am going to use it is there anything I should be careful of?

The code I used:

st$sv <- svobj$sv #st is the sample table. svobj$sv is the sva variables estimated for batch effect correction

ddsTxi.1 <- DESeqDataSetFromTximport(txi,                    #txi is the tximport from kalisto of a cancer patient cohort
                                   colData = st,
                                   design = ~ 0 + Final.Label + sv)     #Final label is the subtype of the cancer of each patient

# Pre-filtering. Filter out samples with TPM below 2 in less than 4% of the sample (there are some rare subtypes)
library(genefilter)
abundance = txi$abundance   
abs_crit = pOverA(0.04, 2)      
abs_filter <- filterfun(abs_crit)
keep <- genefilter(abundance, abs_filter)
dds.1 <- ddsTxi.1[keep,]

dds.1 <- DESeq(dds.1)

res.1 <- lfcShrink(dds.1, contrast = c(-1/12,-1/12,-1/12,-1/12,1,-1/12,-1/12,-1/12,-1/12,-1/12,-1/12,-1/12,-1/12,0), type = "ashr")

Edit: Thank you Michael for pointing towards the solution here: Warnings when using "ashr" in lfcshrinkage for DESeq2

sva DESeq2 • 276 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 2 days ago
United States

There were some recent support site posts with the same error, and a fix emerged as I remember.

ADD COMMENT
0
Entering edit mode

Hi Michael. Thanks for the heads-up. I actually read some of the posts here and on Biostars regarding to the same error, of which most of them you have replied. It seems like most people tried to fix it by filtering out more genes with low counts but the problem persists if I interpreted what they replied correctly. Do you recall what kind of fix it is? Maybe it is just a few google search away but I have the wrong keywords.

ADD REPLY
1
Entering edit mode

I searched ashr and did a time sort:

https://support.bioconductor.org/post/search/?query=Ashr&order=date

It’s the most recent after this one.

ADD REPLY

Login before adding your answer.

Traffic: 561 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