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User: tanyabioinfo

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tanyabioinfo20
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Posts by tanyabioinfo

<prev • 24 results • page 1 of 3 • next >
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Deseq2 two controls in design experiment
... Hi I am using Deseq2 for Differential gene expression analysis. I have two controls ( but they are not technical replicates) and one patient. I designed the experiment with two controls together. I was wondering what Deseq2 does when two controls are taken together. Does it takes an average of t ...
rnaseq deseq2 written 9 days ago by tanyabioinfo20 • updated 9 days ago by Michael Love21k
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(Closed) pheatmap RNA seq data
... Hi    I am plotting a pheatmap using following line in a R code pheatmap(counts_filtered_df,scale="row",cluster_col=FALSE,cluster_row=TRUE,border_color=NA,show_rownames = T)   I want to extract the row names in the same order as shown in pheatmap and the z scores for them.    So basically a n ...
rnaseq R pheatmap written 5 months ago by tanyabioinfo20
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RNAseq tximport Deseq2
...   HI I am using the tximport module to process the output of Salmon. Then I am using the vst(dds) to normalise the data. I understand that the assay for dds is count. How can I process the abundance(TPM) using the vst so that my TPM data is normalised.  My R code looks: txi <- tximport(files, ...
deseq2 tximport written 14 months ago by tanyabioinfo20 • updated 14 months ago by Michael Love21k
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Comment: A: RNA seq tximport
... Hi Michael   Thanks a lot. My TPM data is showing a lot of variation in terms of trends than RPM. Like the tximport output gives a lot of  variation among the replicates. Can you please help me why this would be happening.   Thanks   Tanya ...
written 15 months ago by tanyabioinfo20
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RNA seq tximport
... Hi I am using Salmon to process my RNA seq data. I just want to confirm that the abundance given as an output by the tximport package corresponds to TPM. Many of the cells (the output of tximport) have a value of zero which is making me think about this. Regards Tanya ...
tximport written 15 months ago by tanyabioinfo20
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tximport gene name
... Hi I am doing the following to get the tximport count  matrix with gene name in the first column txdf <- transcripts(EnsDb.Mmusculus.v79, return.type = "DataFrame") txdf$symbol <- mapIds(EnsDb.Mmusculus.v79, txdf$gene_id, "GENENAME", "GENEID") tx2gene <- as.data.frame(txdf[,c("tx_id","sym ...
tximport written 15 months ago by tanyabioinfo20 • updated 15 months ago by Ed Siefker220
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Comment: A: PCA from TPM
... Hi Michael I am now using the follwoing code: txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion=TRUE,dropInfReps=TRUE) sampleTable <- data.frame(condition =samples$condition,time=factor(samples$time)) rownames(sampleTable) <- colnames(txi$counts) dds <- DESeqDataSe ...
written 15 months ago by tanyabioinfo20
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PCA from TPM
... Hi I am trying to do PCA analysis of my samples. I generated the matrix using the tximport package. I have transcript ids as my rows and the sample names are the columns. txi <- tximport(files, type="salmon", tx2gene=NULL, ignoreTxVersion=TRUE,dropInfReps=TRUE,txOut = TRUE) tpm <- (txi$abun ...
pca tpm tximport written 15 months ago by tanyabioinfo20
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Answer: A: RNA seq tximport
... Thanks James It worked for me.   ...
written 15 months ago by tanyabioinfo20
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RNA seq tximport
... Hi   I am using the following commands to run tximport txi <- tximport(files, type="salmon", tx2gene=tx2gene,ignoreTxVersion=TRUE,dropInfReps=TRUE) my tx2gene dataframe looks like this              tx_id            gene_id 1 ENSMUST00000082387 ENSMUSG00000064336 2 ENSMUST00000179436 ENSMUSG0 ...
tximport written 15 months ago by tanyabioinfo20

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Popular Question 6 months ago, created a question with more than 1,000 views. For RNA Seq data analysis using Salmon and tximport

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