User: an.anand233

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an.anand23330
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Posts by an.anand233

<prev • 6 results • page 1 of 1 • next >
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Apply the plotPCA function in DESeq2 package to quantitative MS-based data
... Hi guys, I wonder if someone has succeeded to apply the plotPCA function to group samples of Mass Spectrometry (MS) based data such as quantitative proteomics. I like much of the hierarchical clustering and PCA ploting functions implemented in DESeq2, but it seems the inputs of these functions are ...
deseq2 written 3.4 years ago by an.anand23330 • updated 3.4 years ago by chris86380
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Comment: C: DESEQ2--compare two log2-transformated fold changes
... Great, I will try disabling the LFC shrinkage, using the same design but altHypothesis. I think lfcThresold is same with the default (0) or weak (e.g. 0.05) for testing the equality. Many thanks. ...
written 3.6 years ago by an.anand23330
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Comment: C: DESEQ2--compare two log2-transformated fold changes
... Thanks very much for the classification. I am bad in this statistical thoughts. So p-value<alpha we can reject the null hypothesis of the quality, but p-value>alpha we can NOT accept the hypothesis. Does this mean we need another test and set the null hypothesis to be B/A ≠ D/C and see if this ...
written 3.6 years ago by an.anand23330
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Answer: A: DESEQ2--compare two log2-transformated fold changes
... Hi Mike, thank you very much for your detail suggestion. I have tested running this design with my data. Just have a couple of more questions to be classified: 1) the interaction term  geno2:geno3 is to test if the effect of geno2 is equal or different in  geno3 1 vs geno3 2?  if equal, "geno22.geno ...
written 3.6 years ago by an.anand23330
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Answer: A: DESEQ2--compare two log2-transformated fold changes
... Hi Michael, Thanks for a reply.  I think it's possible to split the conditions (different time point) into two separate datasets and let one dataset has only one factor (genotype) ; I read the DESeq2 manual, but it seems most examples are dealing with lineal model, like comparing (A+B) to (C+D). Bu ...
written 3.6 years ago by an.anand23330
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DESEQ2--compare two log2-transformed fold changes
... Hi Folks, I have some RNA-seq datasets from four genotypes (A, B, C, D) and two conditions (time1 and time2). Each genotype in each condition has three replicates. I  would like to compare whether log2(A/B) equals log2(C/D) or not. Does someone have suggestions on how to implement this test in DESe ...

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Popular Question 3.3 years ago, created a question with more than 1,000 views. For DESEQ2--compare two log2-transformed fold changes
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Apply the plotPCA function in DESeq2 package to quantitative MS-based data

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