User: stan

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stan50
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50
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New User
Location:
Pretoria, South Africa
Last seen:
1 week, 5 days ago
Joined:
2 years, 10 months ago
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Posts by stan

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Strange MA-plot using DESeq2
... [Here][1] is the scatter plot of the raw counts between one VC and LTNP samples. [1]: https://s17.postimg.org/7fnrztkfj/Scatter_Plot_VCvs_LTNP_1.png ...
written 12 weeks ago by stan50
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Comment: C: Strange MA-plot using DESeq2
... > sizeFactors(dds) EC_1.count EC_2.count EC_3.count LTNP_1.count 4.69209178 4.68776603 4.46989074 5.10407662 LTNP_2.count LTNP_3.count LTNP_4.count VC_1.count 4.88086201 3.97763836 6.47169000 0.07196773 VC_2.count V ...
written 12 weeks ago by stan50 • updated 12 weeks ago by WouterDeCoster13k
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Comment: C: Strange MA-plot using DESeq2
... I used raw counts generated using HTSeq. I think my design is OK, it's as follows: ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~condition) I only have one variable "condition", which has three levels (EC, VC, LTNP). ...
written 12 weeks ago by stan50
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Comment: C: Strange MA-plot using DESeq2
... I just followed the steps as outlined in the DESeq2 manual. Could there be a problem with my group "VC" samples? which is causing the 99% variance? ...
written 12 weeks ago by stan50
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Comment: C: Strange MA-plot using DESeq2
... I have added the analysis steps. These are samples from HIV-positive individuals grouped according to viral load ...
written 12 weeks ago by stan50
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Strange MA-plot using DESeq2
... Hello, I am using DESeq2 to perform some differential expression analysis between 3 levels of a disease condition. However, I am getting a strange looking MA-plot when i compare some of the conditions. I am trying to understand what could be the reason for the skewness in my MA-plot. Any help will ...
R deseq2 rna-seq written 12 weeks ago by stan50 • updated 5 weeks ago by Biostar ♦♦ 10
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Answer: A: Deseq2: Time series experiment with 2 conditions and 5 time points
... So, I found the answer for my question in one of the Deseq2 threads at the bioconductor support forum, a nice explanation is given and the thread is found here: https://support.bioconductor.org/p/65676/#66860 incase it might be of use to someone else. ...
written 22 months ago by stan50
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Deseq2: Time series experiment with 2 conditions and 5 time points
... Hi all, I have done a time series analysis using the steps outlined below and I got differentially expressed genes showing a condition-specific effect (according to the example at http://www.bioconductor.org/help/workflows/rnaseqGene/#time) > sampleTable<-data.frame(sampleName=sampleFiles, ...
R deseq2 rna-seq written 22 months ago by stan50 • updated 8 days ago by deni.ribicic0
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Comment: C: Deseq2 error using HTSeq input for 10 samples with 3 replicates each
... Thanks guys, that fixed it!! ...
written 22 months ago by stan50
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Deseq2 error using HTSeq input for 10 samples with 3 replicates each
... Hi all, I am getting the following error when I run the differential analysis step: dds<-DESeq(ddsHTSeq) Error in validObject(object) : invalid class "DESeqDataSet" object: factors in design formula must have samples for each level. this error can arise when subsetting a DESeqDataSet, in w ...
R rna-seq written 22 months ago by stan50

Latest awards to stan

Popular Question 3 months ago, created a question with more than 1,000 views. For Deseq2 error using HTSeq input for 10 samples with 3 replicates each
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Deseq2: Time series experiment with 2 conditions and 5 time points
Popular Question 14 months ago, created a question with more than 1,000 views. For Deseq2: Time series experiment with 2 conditions and 5 time points
Scholar 22 months ago, created an answer that has been accepted. For A: Deseq2: Time series experiment with 2 conditions and 5 time points

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