How To Input Missing Values For A Marker In Dexseq
1
3
Entering edit mode
9.5 years ago
venks ▴ 730

Hi,

I have 100 samples (individuals) and 100 (SNPs) genotyped. I call the SNPs either a WildType (WT) or a Rare-variant (RV) across all samples. Few SNPs in a sample had very poor quality. So It is a missing value. I read in this case/control information as matrix. How do we read the missing value in DEXSeq analysis ??? Should I set them to '0' or just leave it blank?

rnaseq • 2.2k views
ADD COMMENT
0
Entering edit mode

Could you maybe give some more information? Are you looking for the effect of the rare variants on differential exon usage? Are you suspecting that the genes harboring (or near) the variants will show a difference, or are the variants in a gene that affects splicing?

ADD REPLY
3
Entering edit mode

I am looking for the effect of rare variant. My question is very straightforward. What do DEXSEQ expect to see when one of my marker/SNP is not called for one particular sample (because we are not sure if it is genotyped right for a certain sample) but is called a RV or WT for all other samples. Does DEXSEQ expect a "BLANK SPACE" or <na> or 0

ADD REPLY
0
Entering edit mode

Sorry, but your reply isn't helpful. Are you trying to use a design matrix with 100 factors (wherein the appropriate sample->factor assignment is occasionally unknown)? That's the most intelligible thing I can make from what you've written. If that's correct, then please edit your question above to make this explicit. If that's not what you're trying to do, then edit your question to EXPLICITLY state EXACTLY what you're trying to do ("looking for the effect of rare variant" is largely meaningless).

ADD REPLY
1
Entering edit mode

I am sorry. Actually I am trying to find the differential exon usage having beadxpress genotyping data. But I guess it is not relevant to my question. Again my question is how do we input a missing case/control information in DEXSEQ. But I guess I figured it out. In DESEQ we give 0 for a no call.. Since DEXSEQ is from the same developers I guess DEXSEQ also requires 0.

Thanks again for your effort to help @dpryan.

ADD REPLY
2
Entering edit mode

DEXSeq use read count from RNA-Seq data. Do you have such data ? otherwise DEXSeq is not suitable.

ADD REPLY
2
Entering edit mode

Yes I have the count data. I was just wondering when I input the case/control information. For eg: SNP123 in sample1 is not called (because of some genotyping error) but the same SNP is called WT/RV for all other samples. How do I input the missing value? Should I leave it as <na> (or) "a blank space" (or) 0. Hope my question makes sense.

Thanks

ADD REPLY
0
Entering edit mode
9.5 years ago
venks ▴ 730

You can input the missing values as 0. But we have to make sure we have specified the conditions in the design else 0 is also considered as a condition variable.

ADD COMMENT

Login before adding your answer.

Traffic: 1337 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