## User: rajeshparmar4

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#### Posts by rajeshparmar4

<prev • 9 results • page 1 of 1 • next >
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... 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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... 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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... 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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... 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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... Thank you so much Kevin. ...
written 8 days ago by rajeshparmar40
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... 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$Batch) plotPCA(vsd, "Batch") after this script. How I will get differential gene expres ... written 9 days ago by rajeshparmar40 2 answers 217 views 2 answers ... Thank you so much. Right now I am not using the ComBat function for my analysis. I am also using the sva package for correcting the batch. The script I used is: #in order to use SVA to remove any effect on the counts from our surrogate variables ddssva <- dds ddssva$SV1 <- svseq\$sv[,1] ddssva ...
written 12 days ago by rajeshparmar40
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... 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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... 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 ...
written 13 days ago by rajeshparmar40 • updated 12 days ago by Yuqing Zhang20

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