User: rajeshparmar4

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Posts by rajeshparmar4

<prev • 11 results • page 1 of 2 • next >
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Comment: C: How to change ensembl ids to gene names before analysis using count table?
... I had analyzed my data by using DESeq2, but I am unable to convert ensembl ids to gene names or gene symbol in dds object. Is it possible to do in DESeq2 before or after runnine DESeq2? ...
written 11 days ago by rajeshparmar40
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How to change ensembl ids to gene names before analysis using count table?
... Hello, I am trying to convert ensembl ids to gene names or gene symbol before analysis. How I will convert this? And how I convert in the results file from DESeq2 or EdgerR?? ...
ensemblid written 12 days ago by rajeshparmar40 • updated 12 days ago by Michael Love26k
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Comment: C: Batch correction by using ComBat function in sva package
... Hello, Can you suggest the right approach for this kind of analysis? Experimental plan: 1. Two groups in which I want differential gene expression: outcome_txt 2. Two batches for the two different experimental dates: Batch It will be very helpful for me If you provide an exact pipeline for the an ...
written 9 weeks ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Yes, I am not able to fully understand the process of batch corrections. I don't have so much experience regarding this, I just started working on RNA seq data. I am trying to analyze my RNA -seq data in which two known batches are there for two dates of experiments. In which, my condition is outco ...
written 9 weeks ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Thank you so much for your response Kevin, OK, then this is not the right way to do the same. Whenever I am using this script and I am getting a higher number of differential gene expression and log2Foldchange is quite high as compare to without sva. The following script is the right way or not?? ...
written 9 weeks ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Hello, Whenever I am using the **SVA to remove the batch effect**, I am getting a higher number of the differential genes as compared to without the removal of batch effects. By using this script on same data: ddssva <- dds ddssva$SV1 <- svseq$sv[,1] ddssva$SV2 <- svseq$sv[, ...
written 9 weeks ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Thank you so much Kevin. ...
written 9 weeks ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Hello Kevin, After adjusting the batch effect by using VST. I am not getting differential gene expression. vsd <- vst(dds) plotPCA(vsd, "Batch") assay(vsd) <- limma::removeBatchEffect(assay(vsd), vsd$Batch) plotPCA(vsd, "Batch") after this script. How I will get differential gene expres ...
written 9 weeks ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Thank you so much. Right now I am not using the ComBat function for my analysis. I am also using the sva package for correcting the batch. The script I used is: #in order to use SVA to remove any effect on the counts from our surrogate variables ddssva <- dds ddssva$SV1 <- svseq$sv[,1] ddssva ...
written 9 weeks ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Thank you so much Kevin for your quick response. I had already used the limma::removeBatchEffect() for removing batch effect in two groups. I had used this script: ##Adjusting for batch effects with VST vsd <- vst(dds) plotPCA(vsd, "Batch") assay(vsd) <- limma::removeBatchEffect(assay(vsd) ...
written 9 weeks ago by rajeshparmar40

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