User: sum732

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sum7320
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Posts by sum732

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Comment: C: Custom post-normalization counts from DESeq2
... Thanks Michael. This helps. ...
written 4 weeks ago by sum7320
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Comment: C: Custom post-normalization counts from DESeq2
... Is there a way to extract normalized counts+regressed SVs (from RUV/SVA). Aim is to use these "normalized" values for clustering such as by TMixClust/degReport. ...
written 5 weeks ago by sum7320
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Comment: C: Custom post-normalization counts from DESeq2
... Hi Micahel, I ran DESeq2 with two design models: `design(ddsMat_MouseAgesmartsva) <- ~ SV1+SV2+SV3+SV4 + Age` and `design(ddsMat_MouseAgesmartsva) <- ~ Batch + Age` Next used following commands to extract the values. However, the values are exactly the same. I thought that with SVs added t ...
written 5 weeks ago by sum7320
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Comment: C: Custom post-normalization counts from DESeq2
... Hi Michael, Thank you replying. I think I was not clear in my question above. I "do not" want to remove any thing. once I have added the SV: `design(ddsMat_MouseAgesmartsva) <- ~ SV1+SV2+SV3+SV4 + Age ` and carried on with downstream steps to perform DGE. Is there a way to extract the "norma ...
written 5 weeks ago by sum7320
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Custom post-normalization counts from DESeq2
... Hello, I will refer to two posts (links below), whereby similar question had been asked in the past: "How to extract normalized counts with covariates in the design" and there was no direct way to get the desired output. https://support.bioconductor.org/p/69992/, https://support.bioconductor.org/ ...
deseq2 covariate deg written 5 weeks ago by sum7320 • updated 5 weeks ago by Michael Love24k
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael. I will into stageR and ImpulseDE2.  ...
written 8 months ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael as suggested I will and perform pairwise analysis and then look at stageR.  One thing that is still confusing me was when I did performed LRT test as you had suggested. Why did the comparisons was with age12M?  [1] "Intercept"      "Age_M18_vs_M12" "Age_M21_vs_M12" "Age_M6_vs_M12" ...
written 8 months ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael and apologies for any confusion.  Perhaps restating will be helpful.  I have samples with replicates for diff time periods (age) and no condition. I want to perform DGE and capture genes that have changed across the ages. Use of LRT was suggested ddsMat_MouseAge<-DESeqDataSetFr ...
written 8 months ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Michael for the response. I do get the part of seeing a single coefficients and use of name in results to get the LFC, p and q among other stats. The values shown must be element of resultsNames(object). Looking at the output from resultsName, the comparison is against M12. This is after us ...
written 8 months ago by sum7320
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Comment: C: DESeq2 Time Series and "control" condition
... Thanks Simon, But "18M", "12M"  etc should be level? and from  ​resultsNames(dds) We know they are not. Only following are:  "Age_M18_vs_M12" "Age_M21_vs_M12" "Age_M6_vs_M12"  ...
written 8 months ago by sum7320

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