User: amirmehrgou

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Posts by amirmehrgou

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Comment: C: How can Differentially Expressed Genes be found by limma package after removing
... As you suggested I utilized removeBatchEffect function in limma package. However, at the time of finding differentially expressed genes I encountered the same errors as I had observed when sva package was used. My codes and errors are as follow: > allB <- removeBatchEffect(as.matrix(all) ...
written 11 days ago by amirmehrgou0
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Comment: C: How can Differentially Expressed Genes be found by limma package after removing
... I was not aware of this method of code writing. Thank you for your guidance. ...
written 11 days ago by amirmehrgou0
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How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
... I wish to raise a question regarding the detection of differentially expressed genes from combined datasets. So as to merge two expression microarray datasets, following the combination of series matrices and their corresponding annotation files, I used the ComBat function in sva package to remove ...
R sva limma batch effect written 12 days ago by amirmehrgou0 • updated 12 days ago by RamRS27k
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Comment: C: Differentially Expressed Genes in merged datasets; How can the differentially ex
... Thank you for specifying your time to help me. Although I know how to gain differentially expressed genes in each array dataset separately since I am a beginner in bioinformatics I have no idea how to perform according to your suggestion (meta-analysis). If it is possible for you I kindly request y ...
written 12 days ago by amirmehrgou0
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Differentially Expressed Genes in merged datasets; How can the differentially expressed genes be found following removing the batch effect?
... Dear friends, I hope you are well. After an almost long coding in R using several packages, on top of which was Limma, I prospered to combine two datasets and remove the batch effect from them. However, in performing R codes as for finding differentially expressed genes in these datasets I encounte ...
R batch-effect degs meta-analysis written 21 days ago by amirmehrgou0 • updated 21 days ago by ATpoint36k

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