User: rajeshparmar4

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Posts by rajeshparmar4

<prev • 9 results • page 1 of 1 • next >
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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 7 days 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 8 days 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 8 days 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 8 days ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Thank you so much Kevin. ...
written 8 days 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$Batch) plotPCA(vsd, "Batch") after this script. How I will get differential gene expres ...
written 9 days ago by rajeshparmar40
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Comment: C: Batch correction by using ComBat function in sva package
... Thank you so much. Right now I am not using the ComBat function for my analysis. I am also using the sva package for correcting the batch. The script I used is: #in order to use SVA to remove any effect on the counts from our surrogate variables ddssva <- dds ddssva$SV1 <- svseq$sv[,1] ddssva ...
written 12 days 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 12 days ago by rajeshparmar40
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Batch correction by using ComBat function in sva package
... I am working on RNA-seq data analysis, I have 2 known batches (two different days for RNA sequencing) for my analysis. I run the ComBat function to remove the batch effect on normalized dds from DESeq2 or unnormalized dds. Now, I am unable to do create the DESeqDataSet from combat_edata for further ...
deseq2 combat tutorial knownbatcheffect written 13 days ago by rajeshparmar40 • updated 12 days ago by Yuqing Zhang20

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