User: bgraphit

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bgraphit20
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United States
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3 months, 1 week ago
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Posts by bgraphit

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Job: Scientist III/IV - Bioinformatics, Cancer Immunology-195107 Boehringer Ingelheim Pharmaceutical Ridgefield,CT USA
... Apply Here: https://tas-boehringer.taleo.net/careersection/global+template+career+section+28external29/jobdetail.ftl?job=195107&tz=GMT-04%3A00 BS/MS Level only NO PHD **Job Description - Scientist III/IV - Bioinformatics, Cancer Immunology (195107)** Boehringer Ingelheim is an equal opportun ...
R cancer immunology job single cell genomics written 3 months ago by bgraphit20
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Comment: C: ERCC and hg19 Bowtie Indexes
... no reason i could use either... could you help me figure out the index situation then ? ...
written 3.8 years ago by bgraphit20
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Comment: C: MA plot from my data frame
... Actually yes it worked. It was my mistake that when I loaded the rdata file that had my list of genes of interest it had a res2 object derived from a .csv file that overwrote over the res2 I needed. Thanks!! ...
written 4.1 years ago by bgraphit20
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Comment: C: MA plot from my data frame
... >genesOfInterest <- as.character(Merged_Genes_in_H3K9me3[1:nrow(Merged_Genes_in_H3K9me3), 1]) > genesOfInterest   [1] "ABCA11P"       "ABCA13"        "ABI3BP"        "ADCY2"           [5] "AMN1"          "ANKMY1"        "ANKRD20A12P"   "ANKRD20A9P"      [9] "ANKRD30BP2"    "ANKRD36BP1"    ...
written 4.1 years ago by bgraphit20
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Comment: C: MA plot from my data frame
... ok so i did res2 <- results(dds) > dim(res2) [1] 25369     7 dar <- res2[rownames(res2) %in% Merged_Genes_notin_H3K9me3$gene, ] > names(Merged_Genes_in_H3K9me3)   [1] "gene" and  the problem is that dar > dar [1] gene           baseMean       log2FoldChange lfcSE          stat ...
written 4.1 years ago by bgraphit20
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Comment: C: MA plot from my data frame
... My genesofInterest list looks like this: > Merged_Genes_notin_H3K27                         gene                    samplex     ...... 2                       A1BG                      0.000000 3                       A1CF                      0.000000 4                       AAAS               ...
written 4.1 years ago by bgraphit20
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Comment: C: MA plot from my data frame
... Hi Steven I am using DESeq2 but I extracted the information from "dr" which is the results (dds) I saved this as a csv. Opened another R session and loaded "dr" where I can have the column with gene name. I changed the header of that column to "gene" then merged "dr" by "gene" it to my list of ge ...
written 4.1 years ago by bgraphit20
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MA plot from my data frame
... Hello! I am trying to figure out how I can make an MA plot from the following my data frame "dar" I am currently using DESeq2 but I extracted the information from data frame "dr" which is the results (dds) I saved this as a csv. Opened another R session and loaded "dr" where I can have the column ...
R plotma written 4.1 years ago by bgraphit20
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Comment: C: Make 2 boxplot from a data frame by plotting values in 1 row with different col
... Within my libraries there are some that have 0 counts so when trying to find the residual to mean from those libraries for that particular gene... there are some that end up being negative values. These are being excluded from the plot when I do the log transformation.  Yet following your advise an ...
written 4.1 years ago by bgraphit20
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Comment: C: Make 2 boxplot from a data frame by plotting values in 1 row with different col
... I am running into the problem where my  data ( residual from mean ... meaning x value - mean) is a series of positive and negative values and it appears that with this plot it is excluding these negative values...   data <- unlist(subset(datavr, gene =="IGF1R", select=2:128)) news <- data.f ...
written 4.1 years ago by bgraphit20

Latest awards to bgraphit

Popular Question 3.8 years ago, created a question with more than 1,000 views. For MA plot from my data frame
Popular Question 3.8 years ago, created a question with more than 1,000 views. For R loop for question

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