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 3 months 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 3 months 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 3 months 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 3 months 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 3 months ago by sum7320 • updated 3 months 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 10 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 10 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 10 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 10 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 10 months ago by sum7320

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