售后

normfinder.zip

将所有基因的表达量文件进行预处理:

保留在所有样品中均表达的基因（有参fpkm>1,无参fpkm>0.3，至少fpkm>0）
与比较组合的差异基因进行比较，过滤掉差异基因
根据表达量大小自大到小排序，选取一定数目的基因放入NormFinder进行内参基因的筛选

数据格式准备如下：

具体操作：

1、打开表达量excel表格（准备的数据）

2、打开NormFinder_0953.xla

之后点击启用

之后转到准备的表达量excel文件

点击加载项，出现NormFinder，即说明NormFinder成功载入。

点击NormFinder→点击accept,即出现下面的界面，各参数根据需要填写即可:

 第一行是否是样品名
 第一列是否是基因名
 最后一行是否是组名
 是否log转化
 是否输出最简化格式（如果不勾选，输出结果会包括组内及组间比较结果）

结果如下图：

第一行结果即为最佳内参基因，第三行为最佳内参基因对。

filter_fpkm.xls:按阈值筛选后的输入文件

Ordered.xls: a table is returned where the rows are ordered according to increasing stability value. The table has four columns. First column is the gene name, second column (GroupDif) is a measure of the difference between the groups (two times the maximum of the |dig| terms entering equation C), third column(GroupSD) is the common standard deviation within a group (a weighted average of the estimated intragroup variances ˆσ2ig from equation B), and the fourth column (Stability) contains the stability measure as given by the average of the terms in equation C. An example can be seen in Table 1.

Ordered.xls文件中是gene稳定性排序的结果，第一列是gene_id，第二列是该gene在组间的差异，第三列是该gene在组内的标准差，第四列是稳定性

UnOrdered.xls: In this case the rows have the same order as the file containing the data. This table has the same columns as before and includes the individual standard deviations for each group (IGroupSD) and the individual group differences (the terms ˆσig from equation B and the terms dig entering equation C)

UnOrdered.xls文件中与Ordered.xls文件前4列是一致的，后面单独给出了每组的信息

PairOfGenes.xls: For each combination of two genes the combined stability value from formula (1.10) in the Supplementary Material is calculated. The table produced gives the names of the two genes and the value of Stability. The table only contains combination of genes for which the stability value, from the first run with no genes combined, is below 0.25 (the latter value can be set by pStabLim in the call of Normfinder)

PairOfGenes.xls文件中是两个gene为一个组合计算的稳定性