User: tud55122

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tud5512220
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2 years, 1 month ago
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Posts by tud55122

<prev • 8 results • page 1 of 1 • next >
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Use normalized counts to generate Fold change?
... Hi, Just want to make sure. I have two batches of RNA-seq and am trying to normalize based on housekeeping genes to minimum batch effect. Should I use normalized counts after RUVSeq correction to generate RPKMs and Fold Change? According to the introduction from RUVSeq, original counts are recomm ...
ruvseq rna-seq written 2.3 years ago by tud5512220
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Comment: A: Best way to address different batches of RNA-seq
... Below are the scripts I used. > samples=read.table("Samples.txt",sep="\t",header=T) > counts = readDGE(samples$countf)$counts > noint = rownames(counts) %in% c("__no_feature","__ambiguous","__too_low_aQual" ,"__not_aligned","__alignment_not_unique ...
written 2.3 years ago by tud5512220 • updated 2.3 years ago by genomax70k
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Comment: C: Best way to address different batches of RNA-seq
... Thanks for the reply. My fold change is computed based on counts values. I used edgeR to calculate counts and generated RPKM values. ...
written 2.3 years ago by tud5512220
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Best way to address different batches of RNA-seq
... I did two batches of RNA-seq upon same drug treatment but at different time points on the same cell line. For each time point, I have corresponding DMSO controls. All my Fold Change values are calculated over the corresponding DMSO control. I'm trying to trace the gene expression dynamics upon my dr ...
rpkm sequence batch effect rna-seq fold change written 2.3 years ago by tud5512220 • updated 13 days ago by Biostar ♦♦ 20
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Hierachical cluster analysis using arraytrack select auto scale data?
... I'm doing a hierarchical cluster analysis using arraytrack and I use a RNA-seq Z-score table. In my case, should I select auto scale data or not? I'm a bit confused. I tried both and the clusters look so different. Since the Z-score table is already normalized, I assume that re-normalization is not ...
rna-seq clustering arraytrack written 2.5 years ago by tud5512220
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Comment: C: Warning message: In y/gene.length.kb : longer object length is not a multiple
... Thanks for your reply, guys. Do you know how to fix the problem? Here are the scripts I used d = DGEList(counts=counts, group=samples$condition) d = calcNormFactors(d) length.genes=read.table("gene_length_mouse.txt",sep="\t",header=T) rpkm.gene=rpkm(d, length.genes[length.genes$Gene %in% rownames(d ...
written 3.3 years ago by tud5512220
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Comment: A: Warning message: In y/gene.length.kb : longer object length is not a multiple
... Thanks for your reply, guys. Do you know how to fix the problem? Here are the scripts I used d = DGEList(counts=counts, group=samples$condition) d = calcNormFactors(d) length.genes=read.table("gene_length_mouse.txt",sep="\t",header=T) rpkm.gene=rpkm(d, length.genes[length.genes$Ge ...
written 3.3 years ago by tud5512220 • updated 3.3 years ago by Michael Dondrup46k
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Warning message: In y/gene.length.kb : longer object length is not a multiple of shorter object length? Any ideas?
... Hi, I'm new to RNA-seq analysis. I'm using EdgeR to generate RPKMs.Everything works fine but the last step, there is a warning message saying that: Warning message: In y/gene.length.kb : longer object length is not a multiple of shorter object length When I checked the RPKMs generated ...
rpkm rna-seq edger written 3.3 years ago by tud5512220 • updated 3.3 years ago by Michael Dondrup46k

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