User: ZihaoXing

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ZihaoXing0
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Posts by ZihaoXing

<prev • 12 results • page 1 of 2 • next >
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how to save picture and add title to waterfall GenVisR mutation analyse?
... i have a problem and want to ask a question .how to save picture and add a title to waterfall mutation analyse by GenVisR  package? ...
genvisr waterfall mutation written 13 months ago by ZihaoXing0 • updated 12 months ago by zlskidmore10
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Comment: C: the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC
... thanks ,i hope it can be changed into log2FC in edgeR in future ,otherwise, it is easy to be confused ,because log default as loge rather than log2 in math. ...
written 14 months ago by ZihaoXing0
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the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC same as log2FC in edgeR?
... i found that the fold change of different RNAseq expression analyse results  in edgeR is logFC, log2FC is also often used in other analysed ,i want to know if the logFC is same as log2FC in edgeR ,or it is based on exp(1). ...
limma edger logfc written 14 months ago by ZihaoXing0 • updated 14 months ago by Gordon Smyth39k
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Comment: C: how to output and get the normalization gene expression data (similar to the FPK
... thanks Gordon Smyth ,i try to use the rpkm() function to see the transform results. thanks your advice. hope you work happy and well on your research. ...
written 14 months ago by ZihaoXing0
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Comment: C: why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM
... thanks Gordon Smyth, i will use the logFC value of edgeR or DESeq2 results. ...
written 14 months ago by ZihaoXing0
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Comment: C: why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM
... thanks Udi Landau, i will use the logFC value of edgeR or DESeq2. ...
written 14 months ago by ZihaoXing0
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how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
...   the RNAseq read counts data can do the different RNAseq expression by the DESeq2 and edgeR , but i also want to get the normalization gene expression data such as FPKM data ,and do the later clinical survival analysis with gene expression. can i get the normalization gene expression by edgeR and D ...
edger deseq2 counts tcga fpkm written 14 months ago by ZihaoXing0 • updated 14 months ago by Gordon Smyth39k
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why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
...    i hava the RNAseq coutns data and fpkm data from TCGA, i want to know the fold change of tumor tissue RNAseq expression contrast of normal tissue RNAseq expression ,counts data is the RNA reads number, fpkm data is similar to real RNA expression. i found that the logFC results from DESeq2 and edg ...
edger deseq2 counts fpkm fc written 14 months ago by ZihaoXing0 • updated 14 months ago by Gordon Smyth39k
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Comment: C: can i only analyse some genes different RNAseq expression analyse not the whole
... thanks a lot for your reply, DESseq2 cost more time than edgeR, you say analyse the whole genome can make a better results. some times ,i think that if i need to analyse the whole genome to see a few of genes analyse results ,it is not very convenient. ...
written 14 months ago by ZihaoXing0 • updated 14 months ago by Gordon Smyth39k
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Comment: C: can i only analyse some genes different RNAseq expression analyse not the whole
... yes,sample number is huge,and the whole genome analyse cost a long time , especially  of edgeR. ...
written 14 months ago by ZihaoXing0

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