User: sutturka

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sutturka0
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Posts by sutturka

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Answer: A: Getting data into (and out of) the MSnSet object
... I have a simple counts data corresponding to raw spectral counts. I followed the [msmsTests Vignette][1] and above suggestions and imported data as follows: **Data format: CSV** ``` Accession,Control1,Control2,Treatment1,Treatment2 Protein1,103,16,46,48 Protein2,81,0,1,0 Protein3,81,0,1,0 Protein4, ...
written 4 weeks ago by sutturka0
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Comment: C: DESeq2 complex model matrix and result interpretations
... Thanks. Can you please answer the last question - what is being compared with: results(dds, contrast=list("ResponseResistant")) ...
written 4 months ago by sutturka0
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Comment: C: DESeq2 complex model matrix and result interpretations
... Thank you for the response. Much appreciated. (1) I did the relevel before building the model.matrix and I get the `post_vs_pre` now resultsNames(dds) [1] "Intercept" "ResponseResistant" [3] "ResponseSensitive.pt.n2" "ResponseResistant.pt. ...
written 4 months ago by sutturka0
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DESeq2 complex model matrix and result interpretations
... I am working with a complex experiment design [shown here][1]. I followed the [DESeq2 manual][2] and suggestions in [another post][3] to remove the unpaired samples from my analysis and got the DESeq2 running without any error. I need further suggestions to verify that my understanding/interpretatio ...
deseq2 written 4 months ago by sutturka0 • updated 4 months ago by Michael Love25k
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Comment: C: Complex Design matrix for DE analysis
... Dear Micheal and Aaron, Thank you for the response. I am starting with DESeq2 and next work with limma. I removed the unpaired samples and then able to get it running correctly. I am posting the code below as it may help someone. #Add patients IDs specific to Response r_vec = rep(1:6, eac ...
written 4 months ago by sutturka0
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Complex Design matrix for DE analysis
... I am working with a complex experiment design shown below and I am not able to build the appropriate design matrix. I looked through the DESeq2 manual and [this blog][1] and tried different designs and every time I am getting error as "Design matrix not of full rank". ![Design][2] [Link for the im ...
limma edger deseq2 written 4 months ago by sutturka0 • updated 4 months ago by Michael Love25k
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Answer: A: edgeR and batch effect
... RNASeq experiment: Control (3 replicates) and 3 Treatments (3 replicates each). sequencing for 2 replicates of Control sample was performed 2 years later which adds very high sequencing depth and data is generated on different instrument.  Sample_Name Treatment Sample NORM ...
written 21 months ago by sutturka0

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