User: Raheleh

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Raheleh140
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Posts by Raheleh

<prev • 84 results • page 1 of 9 • next >
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
... Thanks @ATpoint. The data is RNAseq. I got read count from someone else but I think this is the approach that has been used to get the read count from fastq data: Fastqs were quality assessed by fastqc, then adaptors and sequences below a Phred score of 20 were trimmed using trimgalore. Reads were ...
written 4 days ago by Raheleh140
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
... no they are from different library, because the sum of readcount for each sample is different. sum(read.count$WT1) [1] 13427116 sum(read.count$WT2) [1] 12775113 sum(read.count$WT3) [1] 13606000 sum(read.count$ACA1) [1] 12969172 sum(read.count$ ...
written 4 days ago by Raheleh140 • updated 4 days ago by RamRS26k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
... This is my data after normalization using DESeq2: WT1 WT2 WT3 ACA1 ACA2 ACA3 ENSMUSG00000022857 6.096555e+01 2.728259e+01 5.443049e+01 7.355503e+02 2.381900e+02 3.323308e+02 ENSMUSG00000094478 9.994352e-01 3.243596e+02 0.000000e+00 ...
written 4 days ago by Raheleh140 • updated 4 days ago by RamRS26k
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Only doing log2 transformation for RNAseq read count data without normalizing by DESeq2 ??!
... Hello all, To normalize my read count data I used 2 different approaches: 1) normalized them with DESeq2 and then transformed them to log2 format. 2) I only transformed the read count data to log2 format (without normalizing using DESeq2). I realized that the outputs are pretty much the same!! C ...
deseq2 readcount rna-seq log2 written 4 days ago by Raheleh140 • updated 4 days ago by ATpoint32k
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(Closed) How to make the boxplot outline black and only keep dots colorful?
... Hello folks, I made this boxplot: ![enter image description here][1] This is the script: p_C <- ggplot(data, aes(x = group, y = Cytotoxic.lymphocytes, color =factor(group)))+geom_boxplot()+geom_quasirandom(width=.1)+labs(y = "CTL /MCP")+theme_bw()+theme(legend.position = "none", plot.titl ...
boxplot R ggplot2 written 7 weeks ago by Raheleh140
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Comment: C: how to plot lollipop in which dots show mean/median for each variable?
... What do you mean? this is the structure of my data: str(m_df_cl2) 'data.frame': 1042110 obs. of 2 variables: $ variable: Factor w/ 15 levels "pS6","S6","BetaCatenin",..: 1 1 1 1 1 1 1 1 1 1 ... $ value : num -1.18 -1.18 -1.18 -1.18 -1.18 ... ...
written 7 weeks ago by Raheleh140
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Comment: C: Why Wilcox.test keep giving (p-val = 0.1) even when there is significant differe
... Thanks! I thought quite other way around. Another concern of mine is: Shouldn't have we the normal distribution of data when we are using a parametric statistical test such as t Test???? ...
written 7 weeks ago by Raheleh140
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Why Wilcox.test keep giving (p-val = 0.1) even when there is significant difference between the data?
... Hello all, I did ssGSEA on my gene expression profile and then as the ssGSEA score are so big I used `ssGSEA.normalize()` in multiGSEA package in r to normalize them. Then I drew boxplot using ggplot2 to see if there is significant different between my 2 groups. This is part of my data: HALLMAR ...
ssgsea ggplot wilcox.test significant level written 7 weeks ago by Raheleh140 • updated 7 weeks ago by Constantine280
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Comment: C: how to plot lollipop in which dots show mean/median for each variable?
... Yes I already did, but I got the same image as the previous one. The stick lines are vertical not horizontal :-( ...
written 8 weeks ago by Raheleh140
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Comment: C: how to plot lollipop in which dots show mean/median for each variable?
... Thank you very much Asaf for keep helping me but this time I got this: ggplot(m_df_cl2, aes(value, variable, group=variable)) + stat_summary(fun.y = 'mean', geom='point') + stat_summary(fun.data = "mean_se", geom = "errorbar")+ coord_flip() ![enter image description here][1] I want *variable* ...
written 8 weeks ago by Raheleh140

Latest awards to Raheleh

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 5 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
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Popular Question 13 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?

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