User: CandiceChuDVM

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Posts by CandiceChuDVM

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Unable to load library DESeq2 (installation of package had non-zero exit status)
... Thanks! It worked! Here is what happened when I replied no trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.5/bit_1.1-12.tgz' Content type 'application/x-gzip' length 243803 bytes (238 KB) ================================================== downloaded 238 KB The downloaded b ...
written 18 months ago by CandiceChuDVM30
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Unable to load library DESeq2 (installation of package had non-zero exit status)
... I was unable to load DESeq2 this morning. I have tried to uninstall R and R Studio then reinstall them, but I still got the same warning when running library(DESeq2): Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[ ...
deseq2 written 18 months ago by CandiceChuDVM30 • updated 18 months ago by Michael Love26k
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Comment: C: DESeq2: would 'contrast' work for serial experiments?
... Yes. I am aware of that section. Just wondering if I can use the multigroup setting (instead of the time course analysis) to achieve the same goal.  ...
written 22 months ago by CandiceChuDVM30
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DESeq2: would 'contrast' work for serial experiments?
... Hi all, I have affected vs control samples collected at three different time points, and I would like to compare differentially expressed miRNAs between affected and control at different time points (t1, t2, t3). Here is my sampleTable: > sampleTable condition timepoints A1_T1 affected ...
deseq2 mirna-seq small rna-seq written 22 months ago by CandiceChuDVM30 • updated 22 months ago by Michael Love26k
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Comment: C: How to generate a PCA scree plot in DESeq2?
... Hi Michael, Thank you for your help! Our RNA-seq research has been published in Scientific Reports: https://www.nature.com/articles/s41598-017-16603-y. Your work and technical supports are appreciated and acknowledged in the references and the acknowledgment section.  ...
written 23 months ago by CandiceChuDVM30
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Comment: C: DESeq2 time course experiments for multigroups comparison (>2 groups)
... Thanks! If I understand correctly, for those genes that have low p-value in the time course experiments, they must express differentially from the control but not necessarily express differentially between rapid and slow? I have picked the top 9 genes with the lowest p-value and got this picture. I ...
written 3.4 years ago by CandiceChuDVM30
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DESeq2 time course experiments for multigroups comparison (>2 groups)
... Hi all, I have RNA-seq data from three groups (rapid, slow, and control) at three timepoints (T1, T2, T3). Each group has three replicates except for the control group. After performing the time course experiments in DESeq2, I got over 1000 DEGs. Now, my simple question is: Are those DEGs (1) beh ...
deseq2 time course rna-seq written 3.4 years ago by CandiceChuDVM30 • updated 3.4 years ago by Michael Love26k
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Answer: A: How to generate a PCA scree plot in DESeq2?
... Hi Micheal, Thank you so much!!! I manage to generate the PCA scree plot by following your instruction. Here is my script:      library(DESeq2)      library(matrixStats)            #How to get PCA plot?      ##how to obtain d.deseq was described in DESeq2 manual            cds=estimateDispersi ...
written 3.4 years ago by CandiceChuDVM30
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How to generate a PCA scree plot in DESeq2?
... Hi all, I've watched this video and wants to visualize the PCA scree plot to check my PCA plot that was generated in DESeq2.  Is there any way I can do it in DESeq2 or in other Bioconductor packages? ...
deseq2 pca pca scree plot written 3.4 years ago by CandiceChuDVM30
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Comment: C: How to resolve length bias and get GO/KEGG pathway for "non-standard" species in
... Hi Nadia, Thank you for your reply. It's good to know that it just won't work. I will try to see if I can pass my own gene2cat to get KEGG work. Thanks, Candice ...
written 3.5 years ago by CandiceChuDVM30

Latest awards to CandiceChuDVM

Popular Question 18 months ago, created a question with more than 1,000 views. For How to generate a PCA scree plot in DESeq2?
Popular Question 18 months ago, created a question with more than 1,000 views. For Unable to load library DESeq2 (installation of package had non-zero exit status)

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