User: Yuya Liang

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Yuya Liang0
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r********@tamu.edu

Posts by Yuya Liang

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Compare more than one factor
... Dear Michael, I have another problem. I was trying to visualize DEGs by heatmap but somehow the graph looks weird. Doesn't have the different expression. df <- as.data.frame(colData(DESeq.ds)[,c("Genotype","Trt")]) mat <- assay(DESeq.rlog) head(rownames(mat)) idx <- rownames(res)[ which(re ...
written 10 weeks ago by Yuya Liang0
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Comment: C: Compare more than one factor
... Thank you, Michael!! I was reading your previous post https://support.bioconductor.org/p/65708/. That's really clearly explaining. After thinking about design matrix, I suddenly understand.     Before reducing= ~ genotype + treatment, should I still set the reference level? ...
written 10 weeks ago by Yuya Liang0
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Comment: C: Compare more than one factor
... Thank you, Michael!  But can I set two different ref level for two genotypes respectively?  DESeq$group <- relevel(DESeq$group, ref = c("4610Control", "RondoControl")) Error in DESeq$group : object of type 'closure' is not subsettable ...
written 10 weeks ago by Yuya Liang0
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Comment: C: Compare more than one factor
... Thank you! I just realized I can simply use `contrast = c("group", "4610Drought", "RondoDrought"` to compare. I have another question. The DEGs I got here, did they compare with their own control first? ((i.e. do 4610Drought vs 4610Control and RondoDrought vs RondoControl to see what gene different ...
written 10 weeks ago by Yuya Liang0
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Comment: C: Compare more than one factor
... I followed https://support.bioconductor.org/p/67600/#67612 to create group. DESeq.ds$group <- factor(paste0(DESeq.ds$Genotype, DESeq.ds$Trt)) design(DESeq.ds) <- ~ group dds <- DESeq(DESeq.ds) resultsNames(dds)​ But my resultsNames(dds)​ only has: > resultsNames(dds) [1] "Intercept ...
written 10 weeks ago by Yuya Liang0
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Compare more than one factor
...   Hello everyone, I have questions about how to write design for DESeqDataSetFromMatrix and using "name" and "contrast" argument in results(). Here's how my data looks like: > sample_info                    X Genotype     Trt 1     Flood_4610_D14     4610 Control 2     Flood_4610_D14     4610 ...
deseq2 written 10 weeks ago by Yuya Liang0 • updated 10 weeks ago by Michael Love17k
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Comment: C: X-axis of MAplot and lfcShrink
... Thank you!! I got the result. ...
written 6 months ago by Yuya Liang0
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Comment: C: X-axis of MAplot and lfcShrink
... Thank you, Sir! I didn't notice it's 1e+05 instead of 1e-05. Do you happen to know lfcShrink( ) problem? ...
written 6 months ago by Yuya Liang0
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X-axis of MAplot and lfcShrink
... Hi everyone, The X-axis of my plot looks strange. Why the mean of normalized counts is super small? (My X-axis is 1e+01, 1e+05 but demo plot is 1, 100, 10000) Due to the shape of MA plot, I suppose to shrunk the log2 fold changes. I used lfcShrink() to do it but the result doesn't look like a outpu ...
deseq2 written 6 months ago by Yuya Liang0
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Comment: C: Strange MA plot
... Thank you so much, Dr. Love!!! I got the normal MA plot! ...
written 6 months ago by Yuya Liang0

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